PubMed

Nan Fang Yi Ke Da Xue Xue Bao. 2025 Feb 20;45(2):331-339. doi: 10.12122/j.issn.1673-4254.2025.02.14.ABSTRACTOBJECTIVES: To explore the mechanism of Lacticaseibacillus paracasei E6 for improving vinorelbine-induced immunosuppression in zebrafish.METHODS: The intestinal colonization of L. paracasei E6 labeled by fluorescein isothiocyanate (FITC) in zebrafish was observed under fluorescence microscope. In a zebrafish model of vinorelbine-induced immunosuppression, the immunomodulatory activity of L. paracasei E6 was assessed by analyzing macrophage and neutrophil counts in the caudal hematopoietic tissue (CHT), the number of T-lymphocyte, and the expressions of interleukin-12 (IL-12) and interferon-γ (IFN-γ). The contents of short-chain fatty acids (SCFAs) in L. paracasei E6 fermentation supernatant and the metabolites of L. paracasei E6 in zebrafish were detected by LC-MS/MS-based targeted metabolomics. The immunomodulatory effects of the SCFAs including sodium acetate, sodium propionate and sodium butyrate were evaluated in the zebrafish model of immunosuppression.RESULTS: After inoculation, green fluorescence of FITC-labeled L. paracasei E6 was clearly observed in the intestinal ball, midgut and posterior gut regions of zebrafish. In the immunocompromised zebrafish model, L. paracasei E6 significantly alleviated the reduction of macrophage and neutrophil counts in the CHT, increased the fluorescence intensity of T-lymphocytes, and promoted the expressions of IL-12 and IFN-γ. Compared with MRS medium, L. paracasei E6 fermentation supernatant showed significantly higher levels of acetic acid, propionic acid and butyric acid, which were also detected in immunocompromised zebrafish following treatment with L. paracasei E6. Treatment of the zebrafish model with sodium acetate and sodium propionate significantly increased macrophage and neutrophil counts in the CHT and effectively inhibited vinorelbine-induced reduction of thymus T cells.CONCLUSIONS: L. paracasei E6 can improve vinorelbine-induced immunosuppression in zebrafish through its SCFA metabolites acetic acid and propionic acid.PMID:40031977 | DOI:10.12122/j.issn.1673-4254.2025.02.14

Food Chem. 2025 Feb 24;477:143580. doi: 10.1016/j.foodchem.2025.143580. Online ahead of print.ABSTRACTCamellia sinensis var. assamica cultivars 'Zijuan' (ZJ, characterized by high anthocyanin content) and 'Mengku large-leaf' (LL, with high content of catechins) are widely consumed in China. Therefore, when processed into green, white, and black teas, differences in composition and biological activities should be detectable. The aim of this work was to explore these potential differences. To achieve that, in vitro bioactivity assays and metabolomics combined with correlation and ridge analyses were applied. Metabolomics revealed that the concentrations of theasinensins, anthocyanins, and amino acids in ZJ teas were higher than those in LL teas. Compared with green and white teas, black teas had higher concentrations of Amadori rearrangement products and theaflavins. Bioactivity assays showed ZJ teas had stronger bioactivity than LL teas. Catechins, procyanidins, and flavone glycosides were identified as key contributors to bioactivity differences rather than anthocyanins. These results suggested that ZJ was more suitable for making functional tea beverages.PMID:40031135 | DOI:10.1016/j.foodchem.2025.143580

Plant Physiol Biochem. 2025 Feb 26;222:109716. doi: 10.1016/j.plaphy.2025.109716. Online ahead of print.ABSTRACTDrought stress severely limits the growth and productivity of sweet cherry (Prunus avium L.). Dark septate endophytes (DSEs) are a group of root-associated fungi known to enhance plant stress tolerance. This study aimed to explore the role of DSE fungus S16 in improving drought tolerance in sweet cherry seedlings and to reveal the underlying molecular and microbial mechanisms through a multi-omics approach. Physiological analysis showed that S16 inoculation improved plant growth, increased relative water content, photosynthetic rate, and antioxidant enzyme activities, while reducing ion leakage and oxidative damage under drought conditions. Metabolomic and transcriptomic analyses identified key metabolic pathways, particularly flavonoid and phenylpropanoid biosynthesis, as being significantly activated, with upregulation of genes such as PAL, 4CL and CHS, and increased accumulation of metabolites like cinnamic acid (CA) and flavonoid derivatives. Exogenous application of CA at 0.5 mM further enhanced drought resistance by reducing reactive oxygen species (ROS) levels, increasing proline accumulation, and boosting antioxidant enzyme activities. Rhizosphere microbiota analysis revealed that S16 symbiosis and CA treatment under drought conditions increased the abundance of beneficial bacteria, such as members of Sphingomonas, Stenotrophobacter and Parcubacteria, while promoting the dominance of Humicola and Fusarium fungi. These findings provide multi-omics evidence for the role of S16 in enhancing drought tolerance in sweet cherry, offering a theoretical basis for the application of DSE fungi in sustainable fruit tree production.PMID:40031102 | DOI:10.1016/j.plaphy.2025.109716

PLoS One. 2025 Mar 3;20(3):e0315999. doi: 10.1371/journal.pone.0315999. eCollection 2025.ABSTRACTPoor penetration of many anti-tuberculosis (TB) antibiotics into the central nervous system (CNS) is thought to be a major driver of morbidity and mortality in TB meningitis (TBM). While the amount of a particular drug that crosses into the cerebrospinal fluid (CSF) varies from person to person, little is known about the host factors associated with interindividual differences in CSF concentrations of anti-TB drugs. In patients diagnosed with TBM from the country of Georgia (n = 17), we investigate the association between CSF concentrations of anti-TB antibiotics and multiple host factors including serum drug concentrations and CSF concentrations of metabolites and cytokines. We found > 2-fold differences in CSF concentrations of anti-TB antibiotics from person to person for all drugs tested including cycloserine, ethambutol, imipenem, isoniazid, levofloxacin, linezolid, moxifloxacin, pyrazinamide, and rifampin. While serum drug concentrations explained over 30% of the variation in CSF drug concentrations for cycloserine, isoniazid, linezolid, and pyrazinamide (adjusted R2 ≥ 0.3, p < 0.001 for all), there was no significant association between serum concentrations of imipenem and ethambutol and their respective CSF concentrations. CSF concentrations of carnitines were significantly associated with concentrations of ethambutol and imipenem (q < 0.05), and imipenem was the only antibiotic significantly associated with CSF cytokine concentrations. These results indicate that there is high interindividual variability in CSF drug concentrations in patients treated for TBM, which is only partially explained by differences in serum drug concentrations. With the exception of imipenem, there was no association between CSF drug concentrations and concentrations of cytokines and chemokines.PMID:40029856 | DOI:10.1371/journal.pone.0315999

Gut Microbes. 2025 Dec;17(1):2474256. doi: 10.1080/19490976.2025.2474256. Epub 2025 Mar 3.ABSTRACTAtopic dermatitis (AD) is a globally prevalent chronic inflammatory skin disorder. Its pathogenesis remains incompletely understood, resulting in considerable therapeutic challenges. Recent studies have highlighted the significance of the interaction between AD and gut microbiome. In this study, we investigated the effects of probiotic-derived extracellular vesicles on AD. Initially, we isolated and characterized extracellular vesicles from Limosilactobacillus fermentum SLAM 216 (LF216EV) and characterized their composition through multi-omics analysis. Gene ontology (GO) and pathway analysis classified LF216EV proteins into biological processes, molecular functions, and cellular components. Importantly, specific abundance in linoleic, oleic, palmitic, sebacic, and stearic acids indicating upregulated fatty acid metabolism were observed by metabolomic analysis. Furthermore, featured lipid profiling including AcylGlcADG and ceramide were observed in LF216EV. Importantly, in an atopic dermatitis-like cell model induced by TNFα/IFNγ, LF216EV significantly modulated the expression of immune regulatory genes (TSLP, TNFα, IL-6, IL-1β, and MDC), indicating its potential functionality in atopic dermatitis. LF216EV alleviated AD-like phenotypes, such as redness, scaling/dryness, and excoriation, induced by DNCB. Histopathological analysis revealed that LF216EV decreased epidermal thickness and mast cell infiltration in the dermis. Furthermore, LF216EV administration reduced mouse scratching and depression-related behaviors, with a faster onset than the classical treatment with dexamethasone. In the quantitative real-time polymerase chain reaction (qRT-PCR) analysis, we observed a significant increase in the expression levels of htrb2c, sert, and tph-1, genes associated with serotonin, in the skin and gut of the LF216EV-treated group, along with a significant increase in the total serum serotonin levels. Gut microbiome analysis of the LF216EV-treated group revealed an altered gut microbiota profile. Correlation analysis revealed that the genera Limosilactobacillus and Desulfovibrio were associated with differences in the intestinal metabolites, including serotonin. Our findings demonstrate that LF216EV mitigates AD-like symptoms by promoting serotonin synthesis through the modulation of gut microbiota and metabolome composition.PMID:40028723 | DOI:10.1080/19490976.2025.2474256

Plant J. 2025 Mar;121(5):e70040. doi: 10.1111/tpj.70040.ABSTRACTCamellia sinensis is an industrial crop characterized by specific secondary metabolites, which provide numerous benefits to human health. Previous researches reveal that the secondary metabolism of tea plants is significantly affected by various environmental factors, especially light intensity. However, the epigenetic mechanism underlying these high light-induced changes remains systematic research. In this study, physiological analysis suggested that increased photosynthetic product was rapidly converted into other organic compounds in adaptation to high light. The metabolite landscape by widely targeted metabolome revealed 219 differentially accumulated metabolites (DAMs) in high light, with substantial upregulated DAMs accumulated in 'amino acids and derivatives' and 'alkaloids'. The landscape of nine crucial histone modifications showed the distribution diversity in the genome and the complex relationship with gene expression. Integrated analysis of stomatal development, metabolome, epigenome, and transcriptome indicated that the dynamics of histone modifications (H3K4ac, H3K4me3, H3K9ac, H3K9me2, H3K27ac, and H3K27me3) on gene regions were closely related to the expression of regulatory genes in stomatal development and enzyme genes in secondary metabolic pathways, leading to stomatal density and metabolite changes in high light. Furthermore, H3K27ac and H3K27me3 were identified as key histone modifications, regulating critical genes under high light, including CsEPFL9, CsYODAb, CsF3'Hb, CsCHSc, CsANRa, CsDFRb-2, CsAlaDC, CsAAP1, CsGGT2, CsXMPP, Cs7-NMT, CsPORC, and CsPSY. These results suggest the pivotal role of histone modifications in the high light-induced stomatal density and secondary metabolite changes of tea plants.PMID:40028698 | DOI:10.1111/tpj.70040

Cancer Med. 2025 Mar;14(5):e70707. doi: 10.1002/cam4.70707.ABSTRACTAIM: The tumor microenvironment (TME) of non-small cell lung cancer (NSCLC) is highly heterogeneous and is involved in tumorigenesis and resistance to therapy. Among the cells of the TME, endothelial cells are associated with the latter processes through endothelial-to-mesenchymal transition (EndMT). During EndMT, endothelial cells (ECs) progressively lose their endothelial phenotype in favor of a mesenchymal phenotype, which favors the production of cancer-associated fibroblasts (CAFs). Our study aimed to investigate the consequences of exposure to different lung tumor secretomes on EC phenotype and plasticity.MATERIALS AND METHODS: Conditioned media (CM) were prepared from the tumor cell lines A549, H1755, H23, H1437, and H1975. Proliferation and migration of ECs treated with these CMs were assessed by Cyquant and Incucyte technologies, respectively. The angiogenic capacity of ECs was assessed by following tubulogenesis on Matrigel. Phenotypic changes in treated ECs were detected by flow cytometry. Morphological analysis of actin fibers was performed by immunohistochemistry, while proteomic analysis by mass spectrometry was used to identify the protein content of secretomes.RESULTS: A change of the endothelial phenotype was found when human umbilical vein endothelial cells (HUVECs) were treated with different CMs. This phenotypic change was associated with a morphological change, an increase in both stress fiber expression and spontaneous migration. Furthermore, an increase in mesenchymal markers (α-SMA and CD44) confirmed the phenotypic changes. However, the secretomes did not modify the rate of double-labeled cells (vWF+/α-SMA+ or CD31+/CD44+). Proteomic analysis identified potential targets involved in the EndMT with therapeutic relevance.CONCLUSION: Taken together, these data suggest that CMs can induce partial EndMT.PMID:40028673 | DOI:10.1002/cam4.70707

Heliyon. 2025 Feb 5;11(4):e42461. doi: 10.1016/j.heliyon.2025.e42461. eCollection 2025 Feb 28.ABSTRACTBACKGROUND: The chromatographic measurement of polar molecules is often surprisingly complicated. On the one hand, the standard experiments use C18 columns, which is usually unsuitable. On the other hand, these types of molecules can behave vastly differently despite their similarities. Thus, finding the right chromatographic conditions is challenging. HILIC can be an obvious choice, but C18 is still used with suitable analytes. Comparing the two methods would be advantageous, but a numerical comparison can be problematic. Thus, a simple comparing and ranking system is needed and put to use to find the best method for the separation of polar basic molecules.RESULTS: In this paper, nine columns with different stationary phases, from reversed-phase to hydrophilic interaction, are compared and ranked in gradient elution. The effect of pH was also considered. The measurements were repeated in acidic, near-to-neutral, and basic conditions. A straightforward system is developed to rank different stationary phases. Its foundation was peak shapes and resolutions. Every measurement condition with all the columns on the available pHs is evaluated by each property. The testing solution consisted of ten components, which aimed to cover a wide range of polar basic molecules. The comparison also focuses on these analytes. We highlighted which analyte is adaptable to different methods or which needed exclusive conditions. The resulting best column with the optimal conditions is presented and proven highly efficient for their separation.SIGNIFICANCE: A straightforward comparison and ranking system is developed to test multiple chromatographic columns with different stationary phases, from reversed-phase to hydrophilic interaction in gradient elution, seeking the best method for separating polar basic molecules. Nine columns were compared in multiple conditions. The best setup resulting in the competition is presented in detail, which can be applied to a wide range of analytes.PMID:40028593 | PMC:PMC11867270 | DOI:10.1016/j.heliyon.2025.e42461

Front Immunol. 2025 Feb 14;16:1550500. doi: 10.3389/fimmu.2025.1550500. eCollection 2025.ABSTRACTMacrophages, crucial innate immune cells, defend against pathogens and resolve inflammation, maintaining tissue balance. They perform phagocytosis, present antigens to T cells, and bond innate and adaptive immunity through various activation states. Classical activation is associated with Th1 responses and interferon γ production, while alternative activation, induced by interleukin 4, is characterized by increased endocytosis, reduced secretion of pro-inflammatory cytokines, and roles in immunoregulation and tissue remodeling. Although these represent opposite extremes observed in vitro, the remarkable plasticity of macrophages allows for a wide spectrum of activation phenotypes that are complex to characterize experimentally. While the application of omics techniques has resulted in significant advances in the characterization of macrophage polarization, lipidomic studies have received lesser attention. Beyond their role as structural components and energy sources, lipids function as signaling molecules that regulate macrophage activation and polarization, thereby shaping immune responses. This work reviews the interaction between lipid signaling and macrophage polarization, exploring how lipid metabolism influences macrophage phenotype and function. These insights offer potential therapeutic strategies for immune-mediated diseases and inflammation-related disorders, including inflammaging.PMID:40028333 | PMC:PMC11867965 | DOI:10.3389/fimmu.2025.1550500

Front Immunol. 2025 Feb 14;16:1509114. doi: 10.3389/fimmu.2025.1509114. eCollection 2025.ABSTRACTINTRODUCTION: Ulcerative colitis (UC) is often characterized by dysbiosis of the colonic microbiota and metabolic disturbances, which can lead to liver damage. Patchoulene epoxide (PAO), a tricyclic sesquiterpene derived from the aged essential oil of Pogostemonis Herba, is known for its anti-inflammatory and ulcer-healing properties. However, its dual protective role against UC and liver injury remains largely unexplored. This study aims to elucidate the protective effect and underlying mechanism of PAO against dextran sulfate sodium (DSS)-induced UC and liver injury in mice.METHODS: Colitis and liver injury in mice were induced by adding 3% DSS to their drinking water continuously for 7 days, and PAO at the doses of 20 and 40 mg/kg was administered orally to mice daily from the first day until the experimental endpoint. Stool consistency scores, blood stool scores, and body weights were recorded weekly. Disease activity index (DAI) was determined before necropsy, where colon and liver tissues were collected for biochemical analyses. Additionally, the fecal microbiome and its metabolites of treated mice were characterized using 16S rRNA amplicon sequencing and metabolomics.RESULTS: PAO significantly reduced the disease activity index and mitigated colonic atrophy in UC mice. It also improved colonic and hepatic pathological changes by safeguarding tight and adherens junctions, and suppressing the generation of pro-inflammatory cytokines and lipopolysaccharide. These beneficial effects were attributed to PAO's capability to regulate the colonic microbiota and metabolic processes. PAO was found to enhance the diversity of the colonic microbiota and to shift the microbial balance in UC mice. Specifically, it restored the microbiota from an Akkermansia-dominated state, characteristic of UC, to a healthier Muribaculaceae-dominated composition. Furthermore, PAO corrected the colon metabolic disturbance in UC mice by modulating the purine metabolism, notably increasing the abundance of deoxyadenosine, adenosine and guanine in UC mice.CONCLUSIONS: The therapeutic effect of PAO on UC and liver injury was mainly attributed to its regulation of colonic microbiota and purine metabolism. These insights emphasize the overall therapeutic benefits of PAO in treating UC and liver injury.PMID:40028318 | PMC:PMC11868103 | DOI:10.3389/fimmu.2025.1509114

Front Cell Infect Microbiol. 2025 Feb 14;15:1523863. doi: 10.3389/fcimb.2025.1523863. eCollection 2025.ABSTRACTThis study aimed to investigate the relationship between gut microbiota composition, fecal metabolites, and postoperative prognosis in patients with extrahepatic cholangiocarcinoma (eCCA). A total of 53 patients with resectable eCCA and 21 healthy volunteers as a control group were included. 16S rRNA gene sequencing and metabolomic analyses revealed significant differences in the gut microbial community structure and altered fecal metabolites profiles between eCCA patients and healthy controls. Univariate and multivariate Cox regression analyses indicated that factors such as preoperative total bilirubin, indirect bilirubin, and specific metabolites were closely associated with overall survival in patients with eCCA post-surgery. The constructed nomogram model further demonstrated the predictive value of these factors, achieving a C-index of 0.718, with calibration curves confirming its strong predictive performance. In conclusion, gut microbiota composition and fecal metabolites play a crucial role in the surgical prognosis of eCCA patients, providing new insights for clinical prognostic assessment.PMID:40028184 | PMC:PMC11868125 | DOI:10.3389/fcimb.2025.1523863

ACS Omega. 2025 Feb 11;10(7):6368-6384. doi: 10.1021/acsomega.4c03407. eCollection 2025 Feb 25.ABSTRACTPentachlorophenol (PCP) is one of the most common chlorophenols utilized in numerous industrial processes, including the production of dyes, pesticides, wood preservatives, disinfectants, antiseptics, and medicines because it has fungicidal and bactericidal characteristics. Previous studies on catfish (Heteropneustes fossilis) revealed that PCP acts as a potent endocrine disruptor and also causes behavioral changes in a concentration-dependent manner. However, the toxicological effects of PCP have not been compared between male and female catfish. The present study aims to investigate the toxic effects of PCP on catfish through histopathological changes, oxidative stress, and serum metabolomics after 60 days of exposure. Chronic exposure to sublethal concentrations of PCP resulted in significant histopathological alterations in the liver and gonad, including leukocyte infiltration, hepatocyte degeneration, follicular layer dissolution, and abnormal sperm distribution. Increased levels of lipid peroxidation and hydrogen peroxide, along with decreased antioxidant enzyme activity, were observed in PCP-exposed groups. A 1H NMR-based metabolomics approach was employed to investigate the toxic effects of PCP on catfish serum, revealing alterations in various metabolites, including amino acids, organic acids, glucose, cholesterol, and neurotransmitters, in a dose-dependent manner. Multivariate partial least-squares discriminant analysis (PLS-DA) identified metabolic changes associated with oxidative stress, disruption in hormone synthesis and reproduction, disturbance in osmoregulation and membrane stabilization, energy metabolism disorder, amino acid metabolism disorder, and neurotransmitter imbalance in PCP-exposed catfish. This study demonstrates the efficacy of metabolomics in elucidating the toxicity and underlying mechanisms of wood preservatives like PCP, providing valuable insights for risk assessment in toxicology research. Overall, these findings contribute to our understanding of the toxicological effects of PCP exposure on aquatic organisms and highlight the potential of histology, oxidative stress, and metabolomics in assessing environmental contaminants' risks.PMID:40028089 | PMC:PMC11866196 | DOI:10.1021/acsomega.4c03407

bioRxiv [Preprint]. 2025 Feb 17:2025.02.13.638125. doi: 10.1101/2025.02.13.638125.ABSTRACTPoor therapeutic index is a principal cause of drug attrition during development. A case in point is L-asparaginase (ASNase), an enzyme-drug approved for treatment of pediatric acute lymphoblastic leukemia (ALL) but too toxic for adults. To elucidate potentially targetable mechanisms for mitigation of ASNase toxicity, we performed multi-omic profiling of the response to sub-toxic and toxic doses of ASNase in mice. We collected whole blood samples longitudinally, processed them to plasma, and extracted metabolites, lipids, and proteins from a single 20-µL plasma sample. We analyzed the extracts using multiple reaction monitoring (MRM) of 500+ water soluble metabolites, 750+ lipids, and 375 peptides on a triple quadrupole LC-MS/MS platform. Metabolites, lipids, and peptides that were modulated in a dose-dependent manner appeared to converge on antioxidation, inflammation, autophagy, and cell death pathways, prompting the hypothesis that inhibiting those pathways might decrease ASNase toxicity while preserving anticancer activity. Overall, we provide here a streamlined, three-in-one LC-MS/MS workflow for targeted metabolomics, lipidomics, and proteomics and demonstrate its ability to generate new insights into mechanisms of drug toxicity.PMID:40027784 | PMC:PMC11870395 | DOI:10.1101/2025.02.13.638125

bioRxiv [Preprint]. 2025 Feb 17:2025.02.13.637433. doi: 10.1101/2025.02.13.637433.ABSTRACTNuclear factor erythroid 2-related factor 2 (NFE2L2/NRF2) is a critical mediator of the cellular oxidative stress response. Aberrant activation of NRF2 is common in lung and upper aerodigestive cancers, where it promotes tumor initiation and progression and confers resistance to chemotherapy, radiation therapy, and immune checkpoint inhibitors. As such, NRF2 therapeutic inhibitors are actively being sought. We previously reported that the antiparasitic drug Pyrimethamine (PYR) inhibits NRF2 in cell lines and in a NRF2-inducible genetically engineered mouse model. Here we design, synthesize, and define structure-activity relationships across a series of 25 PYR-based derivatives to reveal WCDD115 as a 22-fold more potent inhibitor of NRF2 (57nM versus 1.2µM). PYR is known to inhibit plasmodial and human dihydrofolate reductase (DHFR). We found that WCDD115 inhibits hDHFR with 31-fold greater potency than PYR (144nM versus 4.49µM). Metabolomics showed strong similarities between PYR, WCDD115 and methotrexate. Genetic, pharmacological and metabolic epistasis studies reveal that DHFR inactivation is required for NRF2 suppression by WCDD115 and PYR. Global and targeted proteomics revealed overlapping profiles for WCDD115, PYR and methotrexate, including suppression of NRF2 oxidative stress response and activation of TP53 and the DNA damage response. Therefore, PYR and a novel potent derivative WCDD115 are effective, indirect inhibitors of NRF2 and its antioxidant functions. These data underscore the importance of one- carbon metabolism for the NRF2 signaling pathway and support a new therapeutic strategy to suppress NRF2-driven cancer biology.PMID:40027760 | PMC:PMC11870417 | DOI:10.1101/2025.02.13.637433

bioRxiv [Preprint]. 2025 Feb 17:2025.02.12.637912. doi: 10.1101/2025.02.12.637912.ABSTRACTBACKGROUND: Clustering analysis is a foundational step in exploratory data analysis workflows, with dimensionality reduction methods commonly used to visualize multidimensional data in lower-dimensional spaces and infer sample clustering. Principal Component Analysis (PCA) is widely applied in metabolomics but is often suboptimal for clustering visualization. Metabolomics data often require specialized manipulations such as blank removal, quality control adjustments, and data transformations that demand efficient visualization tools. However, the lack of user-friendly tools for clustering without computational expertise presents a challenge for metabolomics researchers. ClusterApp addresses this gap as a web application that performs Principal Coordinate Analysis (PCoA), expanding clustering alternatives in metabolomics. Built on a QIIME 2 Docker image, it enables PCoA computation and Emperor plot visualization. The app supports data input from GNPS, GNPS2, or user-provided spreadsheets. Freely available, ClusterApp can be locally installed as a Docker image or integrated into Jupyter notebooks, offering accessibility and flexibility to diverse users.RESULTS: To demonstrate the data preprocessing techniques available in ClusterApp, we analyzed two Liquid Chromatography coupled to Tandem Mass Spectrometry (LC-MS/MS) metabolomics datasets: one exploring metabolomic differences in mouse tissue samples and another investigating coral life history stages. Among the dissimilarity measures available, the Bray-Curtis measure effectively highlighted key metabolomic variations and patterns across both datasets. Targeted filtering significantly enhanced data reliability by retaining biologically relevant features, 10,617 in the coral dataset and 7,341 in the mouse dataset while eliminating noise. The combination of Total Ion Current (TIC) normalization and auto-scaling improved clustering resolution, revealing distinct separations in tissue types and life stages. ClusterApp's flexible features, such as customizable blank removal and group selection, provided tailored analyses, enhancing visualization and interpretation of metabolomic profiles.CONCLUSION: ClusterApp addresses the need for accessible, dynamic tools for exploratory data analysis in metabolomics. By coupling data transformation capabilities with PCoA on multiple dissimilarity matrices, it provides a versatile solution for clustering analysis. Its web interface and Docker-based deployment offer flexibility, accommodating a wide range of use cases through graphical or programmatic interactions. ClusterApp empowers researchers to uncover meaningful patterns and relationships in metabolomics data without requiring cumbersome data manipulation or advanced bioinformatics expertise.PMID:40027717 | PMC:PMC11870400 | DOI:10.1101/2025.02.12.637912

World J Hepatol. 2025 Feb 27;17(2):101201. doi: 10.4254/wjh.v17.i2.101201.ABSTRACTLiver cancer, particularly hepatocellular carcinoma (HCC), remains a significant global health challenge due to its high mortality rate and late-stage diagnosis. The discovery of reliable biomarkers is crucial for improving early detection and patient outcomes. This review provides a comprehensive overview of current and emerging biomarkers for HCC, including alpha-fetoprotein, des-gamma-carboxy prothrombin, glypican-3, Golgi protein 73, osteopontin, and microRNAs. Despite advancements, the diagnostic limitations of existing biomarkers underscore the urgent need for novel markers that can detect HCC in its early stages. The review emphasizes the importance of integrating multi-omics approaches, combining genomics, proteomics, and metabolomics, to develop more robust biomarker panels. Such integrative methods have the potential to capture the complex molecular landscape of HCC, offering insights into disease mechanisms and identifying targets for personalized therapies. The significance of large-scale validation studies, collaboration between research institutions and clinical settings, and consideration of regulatory pathways for clinical implementation is also discussed. In conclusion, while substantial progress has been made in biomarker discovery, continued research and innovation are essential to address the remaining challenges. The successful translation of these discoveries into clinical practice will require rigorous validation, standardization of protocols, and cross-disciplinary collaboration. By advancing the development and application of novel biomarkers, we can improve the early detection and management of HCC, ultimately enhancing patient survival and quality of life.PMID:40027561 | PMC:PMC11866143 | DOI:10.4254/wjh.v17.i2.101201

Imeta. 2025 Jan 9;4(1):e266. doi: 10.1002/imt2.266. eCollection 2025 Feb.ABSTRACTPolyunsaturated fatty acid-derived oxylipins regulate systemic inflammation and exert cardiovascular effects, yet their role in ST-segment elevation myocardial infarction (STEMI) remains unclear. Herein, we used targeted metabolomics and machine learning algorithms to develop an oxylipin-based risk model to accurately predict recurrent major adverse cardiovascular events (MACE) after STEMI in two independent prospective cohorts with 2 years of follow-up. The in vivo effects of significant oxylipin predictors were explored via a murine myocardial ischemia‒reperfusion model and functional metabolomics. Among the 130 plasma oxylipins detected in discovery cohort (n = 645), patients with and without recurrent MACE exhibited significant differences in a variety of oxylipin subclasses. We constructed an oxylipin-based prediction model that showed powerful performance in predicting recurrent MACE in the discovery cohort (predictive accuracy: 91.5%). The predictive value of the oxylipin marker panel was confirmed in an independent external validation cohort (predictive accuracy: 89.9%; n = 401). Furthermore, we found that the anti-inflammatory/pro-resolving oxylipin (ARO) predictor panel showed better prognostic performance than the pro-inflammatory oxylipin predictor panel in both cohorts. Compared with the treatment of pro-inflammatory oxylipin predictor panel, combined treatment of six ARO predictors, including 14,15 epoxy-eicosatrienoic acid, 14(15)-epoxy-eicosatetraenoic acid, 12,13-epoxy-octadecenoic acid, lipoxin A4, resolving D1, and 6 keto-prostaglandin F1 showed significant cardiac activities and synergistic metabolic actions in myocardial infarction‒reperfusion model mice. We also mechanistically identified an important role of ARO predictors in restraining ceramide/lysophosphatidylcholine synthesis and inhibiting inflammatory responses. Overall, the present study depicted the landscape of oxylipin profiles in the largest panel of STEMI patients worldwide. Our results also highlight the great potential of bioactive oxylipins in prognostic prediction and therapeutics after STEMI.PMID:40027487 | PMC:PMC11865345 | DOI:10.1002/imt2.266

Imeta. 2025 Feb 21;4(1):e70000. doi: 10.1002/imt2.70000. eCollection 2025 Feb.ABSTRACTCholesterol gallstones (CGS) still lack effective noninvasive treatment. The etiology of experimentally proven cholesterol stones remains underexplored. This cross-sectional study aims to comprehensively evaluate potential biomarkers in patients with gallstones and assess the effects of microbiome-targeted interventions in mice. Microbiome taxonomic profiling was conducted on 191 samples via V3-V4 16S rRNA sequencing. Next, 60 samples (30 age- and sex-matched CGS patients and 30 controls) were selected for metagenomic sequencing and fecal metabolite profiling via liquid chromatography-mass spectrometry. Microbiome and metabolite characterizations were performed to identify potential biomarkers for CGS. Eight-week-old male C57BL/6J mice were given a lithogenic diet for 8 weeks to promote gallstone development. The causal relationship was examined through monocolonization in antibiotics-treated mice. The effects of short-chain fatty acids such as sodium butyrate, sodium acetate (NaA), sodium propionate, and fructooligosaccharides (FOS) on lithogenic diet-induced gallstones were investigated in mice. Gut microbiota and metabolites exhibited distinct characteristics, and selected biomarkers demonstrated good diagnostic performance in distinguishing CGS patients from healthy controls. Multi-omics data indicated associations between CGS and pathways involving butanoate and propanoate metabolism, fatty acid biosynthesis and degradation pathways, taurine and hypotaurine metabolism, and glyoxylate and dicarboxylate metabolism. The incidence of gallstones was significantly higher in the Clostridium glycyrrhizinilyticum group compared to the control group in mice. The grade of experimental gallstones in control mice was significantly higher than in mice treated with NaA and FOS. FOS could completely inhibit the formation of gallstones in mice. This study characterized gut microbiome and metabolome alterations in CGS. C. glycyrrhizinilyticum contributed to gallstone formation in mice. Supplementing with FOS could serve as a potential approach for managing CGS by altering the composition and functionality of gut microbiota.PMID:40027485 | PMC:PMC11865347 | DOI:10.1002/imt2.70000

Imeta. 2025 Feb 14;4(1):e272. doi: 10.1002/imt2.272. eCollection 2025 Feb.ABSTRACTThe gut microbiota influences host immunity and metabolism, and changes in its composition and function have been implicated in several non-communicable diseases. Here, comparing germ-free (GF) and specific pathogen-free (SPF) mice using spatial transcriptomics, single-cell RNA sequencing, and targeted bile acid metabolomics across multiple organs, we systematically assessed how the gut microbiota's absence affected organ morphology, immune homeostasis, bile acid, and lipid metabolism. Through integrated analysis, we detect marked aberration in B, myeloid, and T/natural killer cells, altered mucosal zonation and nutrient uptake, and significant shifts in bile acid profiles in feces, liver, and circulation, with the alternate synthesis pathway predominant in GF mice and pronounced changes in bile acid enterohepatic circulation. Particularly, autophagy-driven lipid droplet breakdown in ileum epithelium and the liver's zinc finger and BTB domain-containing protein (ZBTB20)-Lipoprotein lipase (LPL) (ZBTB20-LPL) axis are key to plasma lipid homeostasis in GF mice. Our results unveil the complexity of microbiota-host interactions in the crosstalk between commensal gut bacteria and the host.PMID:40027481 | PMC:PMC11865341 | DOI:10.1002/imt2.272

Imeta. 2025 Feb 17;4(1):e70002. doi: 10.1002/imt2.70002. eCollection 2025 Feb.ABSTRACTThe rapid growth of microbiome research has generated an unprecedented amount of multi-omics data, presenting challenges in data analysis and visualization. To address these issues, we present MicrobiomeStatPlots, a comprehensive platform offering streamlined, reproducible tools for microbiome data analysis and visualization. This platform integrates essential bioinformatics workflows with multi-omics pipelines and provides 82 distinct visualization cases for interpreting microbiome datasets. By incorporating basic tutorials and advanced R-based visualization strategies, MicrobiomeStatPlots enhances accessibility and usability for researchers. Users can customize plots, contribute to the platform's expansion, and access a wealth of bioinformatics knowledge freely on GitHub (https://github.com/YongxinLiu/MicrobiomeStatPlot). Future plans include extending support for metabolomics, viromics, and metatranscriptomics, along with seamless integration of visualization tools into omics workflows. MicrobiomeStatPlots bridges gaps in microbiome data analysis and visualization, paving the way for more efficient, impactful microbiome research.PMID:40027478 | PMC:PMC11865346 | DOI:10.1002/imt2.70002