PubMed

Environ Microbiome. 2024 Oct 24;19(1):79. doi: 10.1186/s40793-024-00618-w.ABSTRACTBACKGROUND: In China, decline disease with unknown etiology appeared as an epidemic among bayberry trees in the southern area of the Yangtze River. Furthermore, the use of beneficial microbes has been reported to be able to reduce the incidence of this disease, emphasizing the association of this disease with microorganisms. Therefore, it has become critical to uncover the microbiome's function and related metabolites in remodeling the immunity of bayberry trees under biotic or abiotic stresses.RESULTS: The amplicon sequencing data revealed that decline disease significantly altered bacterial and fungal communities, and their metabolites in the four distinct niches, especially in the rhizosphere soils and roots. Furthermore, the microbial communities in the four niches correlated with the metabolites of the corresponding niches of bayberry plants, and the fungal and bacterial networks of healthy trees were shown to be more complex than those of diseased trees. In addition, the role of microbiome in the resistance of bayberry trees to the occurrence of decline disease was justified by the isolation, identification, and characterization of important microorganisms such as significantly enriched Bacillus ASV804, Pseudomonas ASV815 in healthy plants, and significantly enriched Stenotrophomonas ASV719 in diseased plants.CONCLUSION: Overall, our study revealed that the occurrence of decline disease altered the microbiome and its metabolites in four ecological niches in particular rhizosphere soils and roots of bayberry, which provides new insight into the control of bayberry decline disease.PMID:39449039 | DOI:10.1186/s40793-024-00618-w

J Transl Med. 2024 Oct 24;22(1):964. doi: 10.1186/s12967-024-05762-y.ABSTRACTBACKGROUND: Immune checkpoint inhibitors (ICIs) have emerged as a novel and effective treatment strategy, yet their effectiveness is limited to a subset of patients. The gut microbiota, recognized as a promising anticancer adjuvant, is being increasingly suggested to augment the efficacy of ICIs. Despite this, the causal link between the gut microbiota and the success of immunotherapy is not well understood. This gap in knowledge has driven us to identify beneficial microbiota and explore the underlying molecular mechanisms.METHODS: Through 16S rDNA sequencing, we identified distinct gut microbiota in patients undergoing treatment with ICIs. Following this, we assessed the impact of probiotics on anti-PD-1 therapy in bladder cancer using mouse models, employing a multi-omics strategy. Subsequently, we uncovered the mechanisms through which Blautia-produced metabolites enhance antitumor immunity, utilizing untargeted metabolomics and a range of molecular biology techniques.RESULTS: In our research, the LEfSe analysis revealed a significant enrichment of the Blautia genus in the gut microbiota of patients who responded to immunotherapy. We discovered that the external addition of Blautia coccoides hampers tumor growth in a bladder cancer mouse model by enhancing the infiltration of CD8+ T cells within the tumor microenvironment (TME). Further investigations through untargeted metabolomics and molecular biology experiments showed that oral administration of Blautia coccoides elevated trigonelline levels. This, in turn, suppresses the β-catenin expression both in vitro and in vivo, thereby augmenting the cancer-killing activity of CD8+ T cells.CONCLUSIONS: This research provided valuable insights into enhancing the efficacy of PD-1 inhibitors in clinical settings. It was suggested that applying Blautia coccoides and its metabolic product, trigonelline, could serve as a synergistic treatment method with PD-1 inhibitors in clinical applications.PMID:39449013 | DOI:10.1186/s12967-024-05762-y

Hum Reprod. 2024 Oct 24:deae244. doi: 10.1093/humrep/deae244. Online ahead of print.ABSTRACTSTUDY QUESTION: What is the significance of visceral adipose tissue (VAT) in the pathogenesis of polycystic ovary syndrome (PCOS) and its impact on the regulation of metabolic disorders in women with PCOS?SUMMARY ANSWER: We revealed a potentially causal relationship between increased genetically predicted VAT and PCOS-related traits, and found that VAT exhibited impaired glucose metabolism and mitochondrial oxidative phosphorylation (OXPHOS) in women with PCOS.WHAT IS KNOWN ALREADY: PCOS is a common reproductive endocrine disorder accompanied by many metabolic abnormalities. Adipose tissue is a metabolically active endocrine organ that regulates multiple physiological processes, and VAT has a much stronger association with metabolism than subcutaneous adipose tissue does.STUDY DESIGN, SIZE, DURATION: Mendelian randomization (MR) analysis was used to investigate the potential causal association between genetically predicted VAT and the risk of PCOS. Data for MR analysis were extracted from European population cohorts. VAT samples from sixteen PCOS patients and eight control women who underwent laparoscopic surgery were collected for proteomics and targeted metabolomics analyses.PARTICIPANTS/MATERIALS, SETTING, METHODS: PCOS was diagnosed according to the 2003 Rotterdam Criteria. The control subjects were women who underwent laparoscopic investigation for infertility or benign indications. Proteomics was performed by TMT labeling and liquid chromatography-tandem mass spectrometry analysis, and targeted metabolomics was performed by ultra-performance liquid chromatography-tandem mass spectrometry analysis. The key differentially expressed proteins (DEPs) were validated by immunoblotting.MAIN RESULTS AND THE ROLE OF CHANCE: MR analysis revealed a potentially causal relationship between increased genetically predicted VAT and PCOS, as well as related traits, such as polycystic ovaries, total testosterone, bioavailable testosterone, and anti-Müllerian hormone, while a negative relationship was found with sex hormone-binding globulin. Enrichment pathway analysis of DEPs indicated the inhibition of glycolysis and activation of mitochondrial OXPHOS in the VAT of PCOS patients. MR analysis revealed that key DEPs involved in glycolysis and OXPHOS were significantly linked to PCOS and its related traits. Dot blot assay confirmed a significant decrease in glycolysis enzymes PKM2 and HK1, and an increase in mitochondrial Complex I and III subunits, NDUFS3 and UQCR10. Moreover, metabolomics analysis confirmed down-regulated metabolites of energy metabolic pathways, in particular glycolysis. Further analysis of PCOS and control subjects of normal weight revealed that dysregulation of glucose metabolism and OXPHOS in VAT of women with PCOS was independent of obesity.LARGE SCALE DATA: The mass spectrometry proteomics data have been deposited to the iProX database (http://www.iprox.org) with the iProX accession: IPX0005774001.LIMITATIONS, REASONS FOR CAUTION: There may be an overlap in some exposure and outcome data, which might affect the results in the MR analysis.WIDER IMPLICATIONS OF THE FINDINGS: The changes in protein expression of key enzymes affect their activities and disrupt the energy metabolic homeostasis in VAT, providing valuable insight for identifying potential intervention targets of PCOS.STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the National Key Research and Development Project of China (2021YFC2700402), the National Natural Science Foundation of China (82071608, 82271665), the Key Clinical Projects of Peking University Third Hospital (BYSY2022043), and the CAMS Innovation Fund for Medical Sciences (2019-I2M-5-001). All authors report no conflict of interest.TRIAL REGISTRATION NUMBER: N/A.PMID:39448886 | DOI:10.1093/humrep/deae244

Sci Rep. 2024 Oct 24;14(1):25144. doi: 10.1038/s41598-024-77431-5.ABSTRACTPancreatic ductal adenocarcinoma (PDAC) has high mortality and rising incidence rates. Recent data indicate that the gut microbiome and associated metabolites may play a role in the development of PDAC. To complement and inform observational studies, we investigated associations of genetically predicted abundances of individual gut bacteria and genetically predicted circulating concentrations of microbiome-associated metabolites with PDAC using Mendelian randomisation (MR). Gut microbiome-associated metabolites were identified through a comprehensive search of Pubmed, Exposome Explorer and Human Metabolome Database. Single Nucleotide Polymorphisms (SNPs) associated by Genome-Wide Association Studies (GWAS) with circulating levels of 109 of these metabolites were collated from Pubmed and the GWAS catalogue. SNPs for 119 taxonomically defined gut genera were selected from a meta-analysis performed by the MiBioGen consortium. Two-sample MR was conducted using GWAS summary statistics from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4), including a total of 8,769 cases and 7,055 controls. Inverse variance-weighted MR analyses were performed along with sensitivity analyses to assess potential violations of MR assumptions. Nominally significant associations were noted for genetically predicted circulating concentrations of mannitol (odds ratio per standard deviation [ORSD] = 0.97; 95% confidence interval [CI]: 0.95-0.99, p = 0.006), methionine (ORSD= 0.97; 95%CI: 0.94-1.00, p = 0.031), stearic acid (ORSD= 0.93; 95%CI: 0.87-0.99, p = 0.027), carnitine = (ORSD=1.01; 95% CI: 1.00-1.03, p = 0.027), hippuric acid (ORSD= 1.02; 95%CI: 1.00-1.04, p = 0.038) and 3-methylhistidine (ORSD= 1.05; 95%CI: 1.01-1.10, p = 0.02). Two gut microbiome genera were associated with reduced PDAC risk; Clostridium sensu stricto 1 (OR: 0.88; 95%CI: 0.78-0.99, p = 0.027) and Romboutsia (OR: 0.87; 95%CI: 0.80-0.96, p = 0.004). These results, though based only on genetically predicted gut microbiome characteristics and circulating bacteria-related metabolite concentrations, provide evidence for causal associations with pancreatic carcinogenesis.PMID:39448785 | DOI:10.1038/s41598-024-77431-5

Sci Rep. 2024 Oct 24;14(1):25165. doi: 10.1038/s41598-024-76054-0.ABSTRACTThe aim of this study is to perform proteomic and metabolomic analyses in bilateral renal pelvis urine of patients with unilateral uric acid kidney stones to identify the specific urinary environment associated with uric acid stone formation. Using cystoscopy-guided insertion of ureteral catheters, bilateral renal pelvis urine samples are collected. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is employed to identify differentially expressed proteins and metabolites in the urine environment. Differentially expressed proteins and metabolites are further analyzed for their biological functions and potential metabolic pathways through Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In the urine from the stone-affected side, eight differential proteins were significantly upregulated, and six metabolites were dysregulated. The uric acid stone urinary environment showed an excess of α-ketoisovaleric acid and 3-methyl-2-oxovaleric acid, which may contribute to the acidification of the urine. Functional and pathway analyses indicate that the dysregulated metabolites are mainly associated with insulin resistance and branched chain amino acid metabolism.PMID:39448683 | DOI:10.1038/s41598-024-76054-0

NPJ Syst Biol Appl. 2024 Oct 24;10(1):124. doi: 10.1038/s41540-024-00448-z.ABSTRACTGenome-scale metabolic models (GEMs) cover the entire list of metabolic genes in an organism and associated reactions, in a tissue/condition non-specific manner. RNA-seq provides crucial information to make the GEMs condition-specific. Integrative Metabolic Analysis Tool (iMAT) and Integrative Network Inference for Tissues (INIT) are the two most popular algorithms to create condition-specific GEMs from human transcriptome data. The normalization method of choice for raw RNA-seq count data affects the model content produced by these algorithms and their predictive accuracy. However, a benchmark of the RNA-seq normalization methods on the performance of iMAT and INIT algorithms is missing in the literature. Another important phenomenon is covariates such as age and gender in a dataset, and they can affect the predictivity of analysis. In this study, we aimed to compare five different RNA-seq data normalization methods (TPM, FPKM, TMM, GeTMM, and RLE) and covariate adjusted versions of the normalized data by mapping them on a human GEM using the iMAT and INIT algorithms to generate personalized metabolic models. We used RNA-seq data for Alzheimer's disease (AD) and lung adenocarcinoma (LUAD) patients. The results demonstrated that RNA-seq data normalized by the RLE, TMM, or GeTMM methods enabled the production of condition-specific metabolic models with considerably low variability in terms of the number of active reactions compared to the within-sample normalization methods (FPKM, TPM). Using these models, we could more accurately capture the disease-associated genes (average accuracy of ~0.80 for AD and ~0.67 for LUAD) for the RLE, TMM, and GeTMM normalization methods. An increase in the accuracies was observed for all the methods when covariate adjustment was applied. We found a similar accuracy trend when we compared the metabolites of perturbed reactions to metabolome data for AD. Together, our benchmark study shows that the between-sample RNA-seq normalization methods reduce false positive predictions at the expense of missing some true positive genes when mapped on GEMs.PMID:39448682 | DOI:10.1038/s41540-024-00448-z

NPJ Sci Food. 2024 Oct 25;8(1):84. doi: 10.1038/s41538-024-00328-0.ABSTRACTThis study aimed to highlight the molecular and biochemical changes induced by methylglyoxal (MGO) exposure in SH-SY5Y human neuroblastoma cells, and to explore how these changes contribute to its neurotoxicity, utilizing an integrated proteomics and metabolomics approach. Using label-free quantitative nanoLC-MS/MS proteomics and targeted LC-TQ-MS/MS-based metabolomics, the results revealed that MGO exposure, particularly at cytotoxic levels, significantly altered the proteome and metabolome of SH-SY5Y cells. Analysis of proteomics data showed significant alterations in cellular functions including protein synthesis, cellular structural integrity, mitochondrial function, and oxidative stress responses. Analysis of metabolomics and integration of metabolomics and proteomics data highlighted significant changes in key metabolic pathways including arginine biosynthesis, glutathione metabolism, cysteine and methionine metabolism, and the tricarboxylic acid cycle. These results suggest that MGO exposure induced both toxic effects and adaptive responses in cells. MGO exposure led to increased endoplasmic reticulum stress, disruptions in cellular adhesion and extracellular matrix integrity, mitochondrial dysfunction, and amino acid metabolism disruption, contributing to cellular toxicity. Conversely, cells exhibited adaptive responses by upregulating protein synthesis, activating the Nrf2 pathway, and reprogramming metabolism to counteract dicarbonyl stress and maintain energy levels. Furthermore, a set of key proteins and metabolites associated with these changes were shown to exhibit a significant concentration-dependent decrease or increase in their expression levels with increasing MGO concentrations, suggesting their potential as biomarkers for MGO exposure. Taken together, these findings provide insight into the molecular mechanisms underlying MGO-induced neurotoxicity and potential targets for therapeutic intervention.PMID:39448607 | DOI:10.1038/s41538-024-00328-0

Rapid Commun Mass Spectrom. 2024 Dec 30;38(24):e9913. doi: 10.1002/rcm.9913.ABSTRACTRATIONALE: Macrolides are critical antibiotics featuring a macrocyclic lactone core with deoxy sugars. Understanding their gas-phase fragmentation is challenging but essential for improving structural elucidation in mass spectrometry, which has implications for drug discovery and development.METHODS: We used electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS) combined with quantum chemical calculations to investigate the fragmentation pathways of erythromycin A and roxithromycin. This approach helps elucidate the preferred fragmentation routes influenced by protonation sites.RESULTS: Macrolides showed similar fragmentation patterns, including sequential losses of saccharide or amino sugar units and dehydration from the macrocycle core. Multiple competitive pathways were observed, influenced by protonation sites. Computational studies confirmed the most favorable protonation sites and their impact on fragmentation, providing insights into key diagnostic product ions. Subsequent fragments involved rearrangement pathways such as alkene formation and cleavages via remote hydrogen transfers and pericyclic reactions.CONCLUSIONS: Our integrated approach offers a comprehensive understanding of macrolide fragmentation, enhancing structural elucidation and potential applications in drug development. This study advances mass spectrometry analysis of macrolides, contributing to pharmaceutical research by integrating orthogonal annotation methods and fragmentation studies.PMID:39448384 | DOI:10.1002/rcm.9913

Food Microbiol. 2025 Jan;125:104657. doi: 10.1016/j.fm.2024.104657. Epub 2024 Oct 9.ABSTRACTAcetobacter is one of the main species producing fruit vinegar and its tolerance mechanism to citric acid has not been fully studied. This limits fruit vinegar production from high-citric-acid fruits, which are excellent materials for fruit vinegar production. This study analyzed the metabolic differences between two strains of A. tropicalis with different citric acid tolerances using non-targeted metabolomics. Differential metabolites and metabolic pathways analysis showed that the enhanced amino acid metabolism significantly improved the citric acid tolerance of A. tropicalis and the deamination of amino acids may also play a role. In addition, the up-regulated phosphatidylcholine (PC) and N-heptanoylhonoserine lactone indicated decreased membrane permeability and enhanced quorum sensing (QS), respectively. The analysis of the interaction between pathways and metabolites indicated that Gln, Cys, and Tyr contribute to improving citric acid tolerance, which was also confirmed by the exogenous addition. After adding the amino acids, the down-regulated qdh, up-regulated ggt, and improved glutathione reductase (GR) activity in J-2736 indicated that glutathione metabolism played an important role in resisting citric acid, and cellular antioxidant capacity was increased. This study provides a theoretical basis for efficient fruit vinegar production from citric-acid-type fruits.PMID:39448167 | DOI:10.1016/j.fm.2024.104657

J Proteomics. 2024 Oct 22:105336. doi: 10.1016/j.jprot.2024.105336. Online ahead of print.ABSTRACTAlzheimer's disease (AD) is the most common form of dementia, affecting approximately 47 M people worldwide. Histological features and genetic risk factors, among other evidence, supported the amyloid hypothesis of the disease. This neuronocentric paradigm is currently undergoing a shift, considering evidence of the role of other cell types, such as microglia and astrocytes, in disease progression. Previously, we described a particular astrocyte subtype obtained from the 3xTg-AD murine model that displays neurotoxic properties in vitro. We continue here our exploratory analysis through the lens of metabolomics to identify potentially altered metabolites and biological pathways. Cell extracts from neurotoxic and control astrocytes were compared using HRMS-based metabolomics. Around 12 % of metabolic features demonstrated significant differences between neurotoxic and control astrocytes, including alterations in the key metabolite glutamate. Consistent with our previous transcriptomic study, the present results illustrate many homeostatic and regulatory functions of metabolites, suggesting that neurotoxic 3xTg-AD astrocytes exhibit alterations in the Krebs cycle as well as the prostaglandin pathway. This is the first metabolomic study performed in 3xTg-AD neurotoxic astrocytes. These results provide insight into metabolic alterations potentially associated with neurotoxicity and pathology progression in the 3xTg-AD mouse model and strengthen the therapeutic potential of astrocytes in AD. BIOLOGICAL SIGNIFICANCE: Our study is the first high-resolution metabolomic characterization of the novel neurotoxic 3xTg-AD astrocytes. We propose key metabolites and pathway alterations, as well as possible associations with gene expression alterations in the model. Our results are in line with recent hypotheses beyond the amyloid cascade, considering the involvement of several stress response cascades during the development of Alzheimer's disease. This work could inspire other researchers to initiate similar studies in related models. Furthermore, this work illustrates a powerful workflow for metabolite annotation and selection that can be implemented in other studies.PMID:39448026 | DOI:10.1016/j.jprot.2024.105336

Sci Total Environ. 2024 Oct 22:177155. doi: 10.1016/j.scitotenv.2024.177155. Online ahead of print.ABSTRACTTriphenyl phosphate (TPP), a wide-used organophosphate flame retardants (OPFRs), is suspected to be a risk factor for the female-specific cancers, but underlying toxicity mechanisms of environmentally relevant dose exposure remain unclear. Herein, a strategy of spherical covalent organic framework (TPB-BPTP-COF)-assisted laser desorption ionization mass spectrometry (LDI-MS), which benefited from fast analysis speed, facile sample preprocessing, and high throughput, was proposed for unveiling the biomarkers of breast cancer (BC) and the relationship between TPP exposure and progression of BC in mice by serum metabolism analysis. The results displayed that 13 metabolites associated with BC development were up-regulated in experimental group versus healthy control mice. Moreover, long-term exposure to environmentally relevant doses of TPP was found to promote BC, mainly by affecting glycolysis/gluconeogenesis, pyrimidine metabolism, pantothenic acid and CoA biosynthesis, and β-alanine metabolism. This work proved the potential application of COFs as LDI-MS substrates in analyzing complex biological samples, and also revealed the risk of long-term low-dose exposure to TPP in the development of BC.PMID:39447910 | DOI:10.1016/j.scitotenv.2024.177155

Sci Total Environ. 2024 Oct 22:177033. doi: 10.1016/j.scitotenv.2024.177033. Online ahead of print.ABSTRACTGut microbiota is important for host metabolism regulation. Antibiotic exposure disturbs this regulation by affecting the microbiome. Trace levels of antibiotics in water have been widely reported and the impact on gut microbiota remains understudied. We provide evidence of trace antibiotic exposure affecting the host's gut microbiota using a mouse model exposed to trace amounts of azithromycin (AZI) or ciprofloxacin (CIP) in drinking water. AZI exposure in males changed the distribution of gram-positive (Firmicutes and Bacteroidetes) and gram-negative (Proteobacteria, Fusobacteria, and Verrucomicrobia) bacteria at an early age. Both AZI and CIP resulted in abnormal microbiota maturation. Additionally, the production of short-chain fatty acids (SCFAs), including acetate, butyrate, and propionate, in females is affected. Serum hormone and metabolome levels shifted after trace antibiotic exposure. AZI and CIP exposure broadly disrupted original host-microbe interaction relationships between the gut microbiota and SCFAs or serum metabolites. In this study, we demonstrated that trace antibiotic exposure was associated with extensive gut microbiota and metabolism perturbation in mice and that the potential health risks in susceptible populations should be considered.PMID:39447894 | DOI:10.1016/j.scitotenv.2024.177033

Comp Biochem Physiol C Toxicol Pharmacol. 2024 Oct 22:110060. doi: 10.1016/j.cbpc.2024.110060. Online ahead of print.ABSTRACTAir exposure stress can induce stress response of Eriocheir sinensis and affect its normal life activities. The goal of this study was to investigate the effects of water immersion on the recovery of hepatopancreas immune-related enzyme activity, intestinal microbial diversity and metabolic level of Chinese mitten crabs after exposure to air. The results show that immersion can effectively alleviate the adverse effects of air exposure on the antioxidant capacity and immune capacity of Chinese mitten crabs, and the longer the time of immersion, the more obvious the recovery effect. Among them, the levels of aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase and acid phosphatase significantly increased after exposure to air (P < 0.05), reached a peak at 3 h, began to decline after immersion, and returned to a level close to the initial value at 24 h (P < 0.05). In addition, after exposure to air, the glucose and total cholesterol in haemolymph of Eriocheir sinensis were significantly different from the initial values (P < 0.05), gradually recovered to the initial level after re-immersion. However, changes in intestinal flora and hepatopancreas metabolism caused by air exposure did not fully recover after water exposure, and its negative effects did not completely disappear. The sequencing results showed that the species composition and diversity of intestinal microorganisms of Chinese mitten crab changed after air exposure and immersion treatment. The relative abundance of Actinomycetes increased significantly, while that of Proteobacteria and Firmicutes decreased significantly. Metabolomics analysis showed that air exposure and immersion destroyed the metabolic balance of amino acids and carnitine, reduced the level of carnitine metabolism, hindered the absorption of nutrients, and led to the accumulation of harmful substances.PMID:39447852 | DOI:10.1016/j.cbpc.2024.110060

Clin Chim Acta. 2024 Oct 22:120015. doi: 10.1016/j.cca.2024.120015. Online ahead of print.ABSTRACTBACKGROUND: Analysis of urinary organic acids (UOAs) by gas chromatography mass-spectrometry (GC-MS) is widely used in metabolomic studies. It is a complex test with many limitations and pitfalls yet there is limited evidence in the literature to support best practice. This study investigated the impact of drying down time and temperature on the recovery of 16 key analytes from solvent extracts.METHODS: Pooled urine specimens were enriched with organic acids. Urine aliquots (n = 3) were acidified and extracted into diethyl ether and ethyl acetate. Extracts were dried under nitrogen at ambient temperature (25 °C); 40 °C; 60 °C then left for 0; +5; +15 min. Dried extracts were derivatised with N,O,-bis-(trimethylsilyl)trifluoroacetamide prior to analysis by GC-MS. Urine specimens from individuals with biotinidase deficiency, maple syrup urine disease (MSUD) and ketotic hypoglycemia were analysed to demonstrate the potential clinical impact.RESULTS: Recovery of shorter chain hydroxycarboxylic acids decreased significantly when extracts were dried above 25 °C (mean recovery 89 % at 60 °C, p < 0.01) or left under nitrogen post-drying (mean recovery at ambient + 15 min, 40 °C + 15mins and 60 °C + 15mins was 56 %, 12 % and 2 %, respectively, p < 0.01). Whilst dicarboxylic acids/medium chain fatty acids were unaffected by temperature (mean recovery 100 %), prolonged drying reduced recovery (mean recovery 85 % at 60 °C + 15mins, p < 0.01).CONCLUSIONS: Evaporation of solvent extracts with heat and/or prolonged drying under nitrogen results in significant losses of the shorter chain hydroxycarboxylic acids. The evaporation protocol must be carefully controlled to ensure accurate and reproducible results, preventing misdiagnoses and/or misinterpretation of results.PMID:39447825 | DOI:10.1016/j.cca.2024.120015

Biochim Biophys Acta Gen Subj. 2024 Oct 22:130729. doi: 10.1016/j.bbagen.2024.130729. Online ahead of print.ABSTRACTSilica-induced lung damage may be associated with changes in distinct metabolites potentially serving as biomarkers. Due to the lack of metabolomic data from animal models, this pilot study aimed to evaluate changes in markers of inflammation and fibrosis, as well as plasma metabolites in rats at 14 and 28 days after silica instillation. Adult male Wistar rats were administered a single oropharyngeal intratracheal dose of silica suspension or sterile saline in controls. Selected markers of inflammation, oxidative stress, fibrosis, and cell counts in blood and bronchoalveolar lavage fluid have been evaluated. Finally, plasma metabolites were detected using a targeted metabolomics approach with an MxP® Quant 500 kit. Silica instillation induced noticeable inflammatory, oxidative, and fibrotic changes in lung tissue within the first 14 days. During the next two weeks, the shifts in some markers were further accentuated. After exposure to silica, the metabolomic analysis identified significant changes in metabolites associated with lipid metabolism, biogenic amines, amino acid derivatives, carboxylic acids, bile acids, putrescine, glycosylceramides, and acylcarnitines. This pilot study provides initial evidence that significant alterations in plasma metabolite profiles accompany silica-induced lung injury in rats. These findings suggest a possible systemic impact, particularly on lipid metabolism, and indicate the urgent need for a deeper understanding of the metabolic reprogramming associated with silica-induced lung injury to pave the way for the discovery of novel biomarkers.PMID:39447776 | DOI:10.1016/j.bbagen.2024.130729

Life Sci. 2024 Oct 22:123167. doi: 10.1016/j.lfs.2024.123167. Online ahead of print.ABSTRACTProspective prediction from the Australian Institute of Health and Welfare (AIHW) showed a likely incidence of 1 in 23 women diagnosed with gynaecological malignancy, where the incidence of relapse with a drug-resistant clone poses a significant challenge in dealing with it even after initial treatment. Glucose metabolism has been exploited as a therapeutic target under anti-metabolomic study, but the non-specificity narrowed its applicability in cancer. Novel updates over epigenetics as a target in gynaecological cancer offer a rational idea of using this in the metabolic rewiring in mutated glycolytic flux-induced drug resistance. This review focuses on the application of epigenetic intervention at a diagnostic and therapeutic level to shift the current treatment paradigm of gynaecological cancers from reactive medicine to predictive, preventive, and personalised medicine. It presents the likely epigenetic targets that can be exploited potentially to prevent the therapeutic failure associated with glucose metabolism-induced chemotherapeutic drug resistance.PMID:39447732 | DOI:10.1016/j.lfs.2024.123167

Life Sci. 2024 Oct 22:123165. doi: 10.1016/j.lfs.2024.123165. Online ahead of print.ABSTRACTAIMS: Regorafenib, an FDA-approved drug for advanced primary liver cancer (PLC), could provide survival benefits for patients. However, markers for its therapeutic sensitivity are lacking. This study seeks to identify sensitive targets of regorafenib in PLC from the perspective of small molecular metabolites.MATERIALS AND METHODS: Initiated with network pharmacology (NP) to map regorafenib's target landscape and metabolic regulatory network in liver cancer. Subsequently, regorafenib's impact on hepatoma cells was evaluated by flow cytometry, western blotting (WB) and cell viability assay. Advanced metabolomics and lipidomics were employed to elucidate regorafenib's metabolic reprogramming effects in liver cancer. Metabolic enzyme expression was assessed by WB, immunohistochemical and immunofluorescence assays. Ultimately, mendelian randomization (MR) analysis was utilized to investigate the potential causality of sphingolipid metabolism in hepatic cancer.KEY FINDINGS: Regorafenib was observed to inhibit hepatoma cell proliferation and cell cycle progression at G0/G1 phase, resulting in significant alterations in sphingolipid levels. It promoted the significant accumulation of 16:0 dihydroceramide (16:0 dhCer) by upregulating ceramide synthase 6 (CERS6) expression and inhibiting dihydroceramide desaturase 1 (DEGS1) activity. The MR analysis revealed that DEGS1 was a risk factor for the development and progression of liver cancer, while cumulative 16:0 dhCer was a protective factor.SIGNIFICANCE: Sphingolipids, particularly dhCer and regulatory enzymes, may be potential sensitive markers of regorafenib in the treatment of liver cancer, providing new insights for enhancing the treated efficacy of regorafenib in liver cancer.PMID:39447728 | DOI:10.1016/j.lfs.2024.123165

J Ethnopharmacol. 2024 Oct 22:118976. doi: 10.1016/j.jep.2024.118976. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Modified Ma-Xing-Shi-Gan decoction (MMXSGD), a classic prescription from Treatise on Febrile Disease in China, is commonly used to treat Klebsiella pneumoniae (KP) infections in clinical settings.MATERIALS AND METHODS: The aim of this study is to assess the efficacy of MMXSGD in the treatment of pneumonia and investigate its underlying mechanism of action. UHPLC-MS/MS was established to identify the main chemical components of serum after intragastric administration with MMXSGD. A mouse model of pneumonia caused by KP was used to evaluate the therapeutic potential of MMXSGD. The macrophage polarization was analyzed by immunohistochemistry. The cytokine profile was assessed using Luminex assay. Lung transcript and metabolite levels were assessed by transcriptomics and non-targeted metabolomics to analyze potential anti-pneumonia mechanisms and targets.RESULTS: 22 major blood-entry components and 274 MMXSGD-pneumonia-related targets were identified. Compared with the model group, the mortality rate of mice in different dosage groups of MMXSGD was significantly reduced, and pathological lung damage was significantly alleviated. Among them, the low dose of MMXSGD treatment had the best protective effect. Further, MMXSGD treatment could regulates M1/M2 polarization in macrophages and inhibits the production of pro-inflammatory cytokines. The data from transcriptome and metabolome analysis indicate that MMXSGD could regulate inflammation-related pathways (PI3K/AKT, HIF-1, NF-κB pathway) and metabolites to modulate pulmonary inflammation. The results demonstrate that MMXSGD enhances the antibacterial effect in vivo by suppressing inflammation and regulating immunity rather than directly antibacterial effect.CONCLUSION: These findings provide a further assessment of MMXSGD, suggesting that MMXSGD has good therapeutic efficacy in bacterial infectious diseases.PMID:39447714 | DOI:10.1016/j.jep.2024.118976

J Ethnopharmacol. 2024 Oct 22:118988. doi: 10.1016/j.jep.2024.118988. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Panax notoginseng saponin (PNS) has a variety of biological activities, such as improvement of myocardial ischemia, improvement of learning and memory, hypolipidemia, and immunomodulation. However, its protective mechanism on the central nervous system (CNS) is not clear.AIM OF THE STUDY: The present study initially evaluated the possible mechanism of PNS to improve cognitive dysfunction due to chronic sleep deprivation (CSD).MATERIALS AND METHODS: In the present study, we used a modified multi-platform aquatic environment sleep deprivation method to induce a cognitively impaired rat model, and explored the mechanism of action of PNS by integrating serum metabolomics and network pharmacology, which was further verified by molecular docking and experiments.RESULTS: The results showed that PNS significantly shortened the escape latency, increased the target quadrant time and the number of traversing platforms, and attenuated the inflammatory damage in the hippocampal Cornu Ammonis 1 (CA1) region in CSD rats. The non-targeted metabolomics results indicated that 35 biomarkers significantly altered following PNS therapy intervention, with metabolic pathways enriched for the effects of One carbon pool by folate, Riboflavin metabolism, Glycerophospholipid metabolism, Sphingolipid metabolism, Glycerolipid metabolism, Arachidonic acid metabolism, and Tryptophan metabolism. In addition, network pharmacology identified 234 potential targets for PNS intervention in CSD with cognitive impairment. Metabolite-response-enzyme-gene network was constructed by MetaScape and matched with the network pharmacology results to identify a total of five shared targets (LPL, GPAM, HSD11B1, HSD11B2, and SULT2A1) and two metabolic pathways (Sphingolipid metabolism and Steroid hormone biosynthesis). The results of molecular docking revealed that the five active ingredients had good binding ability with the five core targets. qPCR analysis confirmed the ability of PNS to modulate the above five targets.CONCLUSIONS: The combination of metabolomics and network analysis provides a scientific basis for promoting the clinical application of PNS in cognitive impairment.PMID:39447711 | DOI:10.1016/j.jep.2024.118988

Planta Med. 2024 Oct 24. doi: 10.1055/a-2420-0270. Online ahead of print.ABSTRACTThis exploratory study was designed to identify factors implicating microbial influence on medicinal plant metabolomes. Utilizing a whole-microbiome approach, amplicon sequencing was used to identify the makeup of fungal and bacterial assemblages from endophytic (interior) and epiphytic (external) environments in two different sets of congeneric host-plant pairs, with collection of multiple samples of two medicinal plant species (Actaea racemosa, Rhodiola rosea) and two generic analogs (Actaea rubra, Rhodiola integrifolia). Diversity analysis of microbial assemblages revealed the influence of three primary factors driving variance in microbial community composition: host-plant taxonomy, the compartmentalization of microbial communities within discrete plant parts, and the scale of distance (microhabitat heterogeneity) between sampling locations. These three factors accounted for ~ 60% of variance within and between investigated microbiomes. Across all our collections, bacterial populations were more diverse than fungi (per compartment), and microbial density in epiphytic compartments (aerial parts, rhizosphere) were higher than those of endophytes (leaf and root). These comparative data point to key loci associated with variation between congeneric pairs and plant genera, providing insight into the complex and contrasting relationships found within this multi-kingdom coevolutionary relationship. Although reflective of only a limited set of botanical source materials, these data document the richness of a relatively unexplored component of the plant world and highlight the relevance of a whole-microbiome ecology-driven approach to botanical research and directed natural product investigations.PMID:39447601 | DOI:10.1055/a-2420-0270