PubMed

Cell Genom. 2025 Mar 19:100810. doi: 10.1016/j.xgen.2025.100810. Online ahead of print.ABSTRACTDifferential susceptibilities to various diseases and corresponding metabolite variations have been documented across diverse ethnic populations, but the genetic determinants of these disparities remain unclear. Here, we performed large-scale genome-wide association studies of 171 directly quantifiable metabolites from a nuclear magnetic resonance-based metabolomics platform in 10,792 Han Chinese individuals. We identified 15 variant-metabolite associations, eight of which were successfully replicated in an independent Chinese population (n = 4,480). By cross-ancestry meta-analysis integrating 213,397 European individuals from the UK Biobank, we identified 228 additional variant-metabolite associations and improved fine-mapping precision. Moreover, two-sample Mendelian randomization analyses revealed evidence that genetically predicted levels of triglycerides in high-density lipoprotein were associated with a higher risk of coronary artery disease and that of glycine with a lower risk of heart failure in both ancestries. These findings enhance our understanding of the shared and specific genetic architecture of metabolites as well as their roles in complex diseases across populations.PMID:40118068 | DOI:10.1016/j.xgen.2025.100810

Cell. 2025 Mar 14:S0092-8674(25)00209-0. doi: 10.1016/j.cell.2025.02.021. Online ahead of print.ABSTRACTUnderstanding how proteins in different mammalian tissues are regulated is central to biology. Protein abundance, turnover, and post-translational modifications such as phosphorylation are key factors that determine tissue-specific proteome properties. However, these properties are challenging to study across tissues and remain poorly understood. Here, we present Turnover-PPT, a comprehensive resource mapping the abundance and lifetime of 11,000 proteins and 40,000 phosphosites in eight mouse tissues and various brain regions using advanced proteomics and stable isotope labeling. We reveal tissue-specific short- and long-lived proteins, strong correlations between interacting protein lifetimes, and distinct impacts of phosphorylation on protein turnover. Notably, we discover a remarkable pattern of turnover changes for peroxisome proteins in specific tissues and that phosphorylation regulates the stability of neurodegeneration-related proteins, such as Tau and α-synuclein. Thus, Turnover-PPT provides fundamental insights into protein stability, tissue dynamic proteotypes, and functional protein phosphorylation and is accessible via an interactive web-based portal at https://yslproteomics.shinyapps.io/tissuePPT.PMID:40118046 | DOI:10.1016/j.cell.2025.02.021

Nutr Res. 2025 Feb 26;136:15-27. doi: 10.1016/j.nutres.2025.02.004. Online ahead of print.ABSTRACTYeast mannans (YM) are potential prebiotics that may improve laxation. The aim was to evaluate the effects of YM on gastrointestinal symptoms, with a hypothesis of high tolerance. A secondary aim assessed stool frequency. Fecal microbiota composition (16S rRNA gene amplicon sequencing) and targeted urine metabolites (LC-MS/MS) were explored. An ex vivo simulation of digestion and fermentation (6 donors) compared YM to the reference prebiotic inulin followed by an open-label pilot study, with a 1-week baseline and 2-week intervention of 15 g/d of YM. Ex vivo findings showed increased Bacteroides faecis, B. ovatus, Parabacteroides merdae, P. distasonis, Blautia faecis, and Bifidobacterium spp. in response to YM. Participants (n = 20, 71.4 ± 11.0 y) reported no change with YM for burping, constipation, diarrhea, flatulence/gas, nausea, reflux/heartburn, or rumblings/noise, rated from 0 for none to 3 for severe symptoms. Cramping/pain marginally increased from baseline (0.02 ± 0.01) to intervention (0.05 ± 0.02; P = .046), as did distention/bloating (baseline, 0.07 ± 0.03; intervention week 2, 0.15 ± 0.05; P = .037). This high tolerability was explained by the ex vivo finding that YM induced less gas production than inulin (-45%). Stool frequency trended higher with YM (1.53 ± 0.15 stools/d) compared to baseline (1.35 ± 0.11) (P = .079); participants with ≤1 stools/d (n = 8) showed an increase (0.84 ± 0.14 to 1.19 ± 0.32; P = .016). In vivo compositional changes in fecal microbiota suggest increased B. faecis, B. ovatus, P. merdae, and P. distasonis levels in response to YM. Overall, YM elicited specific microbiota modulation with minimal gastrointestinal symptoms and the potential to increase stool frequency, supporting its prebiotic potential. This trial was registered at clinicaltrials.gov (NCT05939336).PMID:40117931 | DOI:10.1016/j.nutres.2025.02.004

Redox Biol. 2025 Mar 8;82:103579. doi: 10.1016/j.redox.2025.103579. Online ahead of print.ABSTRACTBronchopulmonary dysplasia (BPD) is a prevalent chronic respiratory condition in preterm infants with an increasing incidence, severely affecting their survival rate and quality of life. Exploring the underlying mechanisms of BPD helps to develop novel effective therapeutic strategies. In this study, integrated metabolomic analyses of tracheal aspirates (TAs) from BPD infants and non-BPD infants, along with lung tissues from hyperoxia-induced experimental BPD neonatal rats and control rats, demonstrated that BPD was associated with a significant reduction in 3-hydroxyanthranilic acid (3-HAA), which was confirmed to be partly caused by tryptophan-metabolizing enzyme disorders. In vivo and in vitro models were subsequently established to assess the efficacy and underlying mechanisms of 3-HAA in relation to BPD. Compared with the BPD group, 3-HAA nebulization improved lung development and suppressed inflammation in rats. Limited proteolysis-small molecule mapping (LiP-SMap) proteomic analysis revealed the involvement of the ferroptosis pathway in the underlying mechanism by which 3-HAA alleviated hyperoxia-induced BPD injury. Ferroptosis was identified by detecting Fe2+ levels, malondialdehyde (MDA), 4-HNE, total aldehydes, mitochondrial morphology, ferroptosis-associated protein and mRNA expression, and this dysregulation was indeed ameliorated by 3-HAA nebulization in vivo. Furthermore, a combination of LiP-SMap, molecular docking, SPR and Co-IP analyses confirmed that 3-HAA can bind directly to FTH1 and disrupt the nuclear receptor coactivator 4 (NCOA4)-FTH1 interaction. In conclusion, our study is the first to reveal that BPD is linked to the reduction of 3-HAA, and 3-HAA could inhibit the ferroptosis pathway by targeting FTH1, thereby alleviating hyperoxia-induced injury in rats and alveolar type II epithelial cells, highlighting the potential of targeting 3-HAA and ferroptosis for clinical applications in BPD.PMID:40117887 | DOI:10.1016/j.redox.2025.103579

Food Chem. 2025 Mar 14;480:143892. doi: 10.1016/j.foodchem.2025.143892. Online ahead of print.ABSTRACTWhite mold is one of the most common and serious fungal diseases of morel affecting the entire growth cycle. Studies show that when infected, plants defend against pathogens by regulating metabolic responses within their systems. A total of 310 metabolites for infecting Paecilomyces penicillatus in morel mushrooms were identified by UPLC-MS/MS. Most metabolites showed an intuitive downward trend during infection and reached their lowest levels at the third stage. For PCA and HCA, infection period had a significant effect on metabolites, and the second stage was the key turning point for metabolite accumulation in response to disease. Correlation analysis of the top 50 differential metabolites with the highest VIP values screened by OPLS-DA suggested that lipids, nucleotides and their derivatives, sugars, organic acids, phenolic acids and alkaloids may respond synergistically to disease during infection. Taken together, this study provided an entry point for studying white mold pathogenesis in morel.PMID:40117821 | DOI:10.1016/j.foodchem.2025.143892

J Hazard Mater. 2025 Mar 18;491:137989. doi: 10.1016/j.jhazmat.2025.137989. Online ahead of print.ABSTRACTThis study aimed to explore the metabolite profiles of populations engaged in intensive vegetable cultivation and their exposure to pesticides. As urbanization progresses and eating habits evolve, intensive vegetable farming has rapidly expanded; however, this cultivation method poses potential health risks to farmers, particularly due to long-term exposure to "greenhouse gases" in enclosed environments. The study investigated the demographic characteristics of individuals in vegetable-growing areas, collected relevant biological samples, and assessed exposure levels by analyzing pesticide metabolites in urine. The results indicated that the types and concentrations of pesticide metabolites detected in the urine of the exposed group were significantly higher than those in the control group, with notable increases in neonicotinoid metabolites such as dinotefuran (DIN) and thiacloprid. Furthermore, the impact of these pesticides on mammalian organisms was examined through animal experiments, which revealed dynamic changes in the concentration of DIN in mouse serum and urine, providing valuable data on its biological metabolic characteristics. These findings underscore the importance of ongoing disease prevention, pollution control, and the need for enhanced health monitoring and protective measures for agricultural workers.PMID:40117779 | DOI:10.1016/j.jhazmat.2025.137989

Comp Biochem Physiol Part D Genomics Proteomics. 2025 Mar 18;55:101486. doi: 10.1016/j.cbd.2025.101486. Online ahead of print.ABSTRACTAnimals frequently suffer from starvation throughout their life cycle; however, the mobilization and utilization of energy sources can differ. To clarify the fundamental mechanisms underlying energy mobilization and metabolic adjustment in response to food deprivation in the soft-shelled turtle (Pelodiscus sinensis), eighty turtles (initial body weight, 51.81 ± 0.29 g) were subjected to starvation periods of 1 d, 4 d, 8 d, 16 d, and 32 d (referred to as S1, S4, S8, S16, and S32). The results showed that the greatest absolute loss in body composition occurred in moisture, followed by protein and lipid, respectively. Hepatic glycogen contents significantly decreased after 4 days of starvation and then remained stable. Notably, plasma glucose, cholesterol, and free fatty acid contents exhibited significant decreases from S8, while plasma triacylglycerol levels dramatically declined from S4. Gluconeogenesis-related genes (pepck, g6pase) were upregulated in the starving turtles to maintain glucose homeostasis. Comparative analyses between S32 and S1 groups identified a total of 6051 differential genes and 150 differential metabolites, highlighting three overlapping metabolic pathways: glycerophospholipid metabolism, alanine, aspartate, and glutamate metabolism, and taurine and hypotaurine metabolism. Integrative analyses further revealed increased levels of specific metabolites, including phosphatidylcholine, phosphatidylethanolamine, glycerophosphocholine, L-2-aminoethyl seryl phosphate, l-serine-phosphatidylethanolamine, adenyiosuccinate, 5-phosphoribosylamine, and taurine. These metabolites are vital for amino acid-driven gluconeogenesis, cell membrane stability, and mitigating cellular damage resulting from food deprivation. In conclusion, glucose homeostasis was maintained by enhancing gluconeogenesis in P. sinensis during extended periods of starvation, and the activation of lipid and amino acid metabolism represents an adaptive metabolic strategy employed by P. sinensis to cope with starvation conditions.PMID:40117751 | DOI:10.1016/j.cbd.2025.101486

Free Radic Res. 2025 Mar 21:1-13. doi: 10.1080/10715762.2025.2483454. Online ahead of print.ABSTRACTChronic kidney disease (CKD) is a progressive condition marked by persistent kidney damage, leading to high mortality rates and economic burden in advanced stages. Ozone therapy has emerged as a complementary alternative capable of mitigating oxidative stress involved in CKD progression. Ozonated saline solution (OSS) prepared via microbubbling offers enhanced efficacy due to greater ozone dissolution, homogeneity, and stability compared to conventional methods. This study compared the biosafety and efficacy of OSS prepared through bubbling and microbubbling methods in advanced CKD patients. In vitro, hydrogen peroxide (H2O2) concentrations were measured at various doses and times for both methods. In healthy volunteer, biosafety was assessed using TMRE and Annexin V in leukocytes. In CKD patients, TMRE, Annexin V, redox markers (catalase, superoxide dismutase, glutathione system, H2O2, lipoperoxidation), and renal function markers (urea, creatinine, glomerular filtration rate) were evaluated. Microbubbling produced lower H2O2 concentrations in vitro, depending on time and ozone dose. In vivo, both methods increased mitochondrial activity and apoptosis in CKD patient leukocytes. However, microbubbling notably enhanced antioxidant capacity, catalase and superoxide dismutase activity, and redox balance (elevated reduced-to-oxidized glutathione ratio) compared to conventional bubbling. It also showed slight improvements in serum clinical parameters. In conclusion, the microbubbling method demonstrated superior biosafety and therapeutic efficacy in advanced CKD patients, highlighting its potential as a preferred approach in ozone therapy.PMID:40117653 | DOI:10.1080/10715762.2025.2483454

Environ Health Perspect. 2025 Mar 21. doi: 10.1289/EHP15117. Online ahead of print.ABSTRACTBACKGROUND: Some synthetic phenols alter hormonal pathways involved in successful pregnancy and fetal development. Despite high within-subject temporal variability of phenols, previous studies mostly utilized spot urine samples to assess pregnancy exposure. Herein we investigated associations between pregnancy exposure to eight phenols assessed in multiple pooled urine samples and steroid hormones assessed in maternal hair reflecting cumulative hormone levels over the previous weeks to months.METHODS: We assessed phenol-hormone associations in 928 pregnant women from two pooled cohorts recruited in Spain (BiSC, 2018-2021) and France (SEPAGES, 2014-2017), using pools of up to 21 samples each, collected in early pregnancy (median gestational age: 18.0 weeks), as well as hair collected in late pregnancy (BiSC) or at birth (SEPAGES). We measured two bisphenols, four parabens, benzophenone-3, and triclosan along with metabolites of three adrenal (Σcortisol, Σcortisone, 11-dehydrocorticosterone) and two reproductive hormones (progesterone, testosterone). We ran adjusted linear regressions for each exposure-outcome pair and Bayesian Kernel Machine Regression for phenols mixture.RESULTS: Bisphenol S was associated with higher cortisol and 11-dehydrocorticosterone concentrations. Propylparaben was associated with lower levels of cortisol, cortisone, and 11-dehydrocorticosterone, while methylparaben was linked to a reduction in cortisol levels. Interestingly, associations identified for parabens were stronger for women carrying female fetuses. No associations for phenols mixture were detected.CONCLUSIONS: Our study suggests that pregnancy exposure to bisphenol S and some parabens (propyl- and methylparaben) may affect production of maternal corticosteroid hormones that are important for a successful pregnancy and fetal development.PMID:40117576 | DOI:10.1289/EHP15117

Sci Adv. 2025 Mar 21;11(12):eads9182. doi: 10.1126/sciadv.ads9182. Epub 2025 Mar 21.ABSTRACTLipid metabolism and the serine, one-carbon, glycine (SOG) and methionine pathways are independently and significantly correlated with estrogen receptor-negative breast cancer (ERneg BC). Here, we propose a link between lipid metabolism and ERneg BC through phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in the de novo serine pathway. We demonstrate that the metabolism of the paradigmatic medium-chain fatty acid octanoic acid leads to a metabolic shift toward the SOG and methionine pathways. PHGDH plays a role in both the forward direction, contributing to the production of S-adenosylmethionine, and the reverse direction, generating the oncometabolite 2-hydroxyglutarate, leading to epigenomic reprogramming and phenotypic plasticity. The methionine cycle is closely linked to the transsulfuration pathway. Consequently, we observe that the shift increases the antioxidant glutathione, which mitigates reactive oxygen species (ROS), enabling survival of a subset of cells that have undergone DNA damage. These metabolic changes contribute to several hallmarks of cancer.PMID:40117373 | DOI:10.1126/sciadv.ads9182

Sci Adv. 2025 Mar 21;11(12):eadr1538. doi: 10.1126/sciadv.adr1538. Epub 2025 Mar 21.ABSTRACTDecreased nicotinamide adenine dinucleotide (oxidized form) (NAD+) levels are reportedly associated with several aging-related disorders. Thus, supplementation with NAD+ precursors, such as nicotinamide mononucleotide (NMN) and nicotinamide riboside (NR), exhibits beneficial effects against these disorders. However, the in vivo metabolic pathways of NMN and NR remain to be elucidated. In this study, we comprehensively analyzed the fate of orally and intravenously administered NMN and NR in mice using NAD+ metabolomics. We found that only a small portion of orally administered NMN and NR was directly absorbed from the small intestine and that most of them underwent gut microbiota-mediated deamidation and conversion to nicotinic acid (NA). Moreover, intravenously administered NMN and NR were rapidly degraded into nicotinamide and secreted to bile followed by deamidation to NA by gut microbiota. Thus, enterohepatic circulated NA is preferentially used in the liver. These findings showed that NMN and NR are indirectly converted to NAD+ via unexpected metabolic pathways.PMID:40117359 | DOI:10.1126/sciadv.adr1538

J Proteome Res. 2025 Mar 21. doi: 10.1021/acs.jproteome.4c00990. Online ahead of print.ABSTRACTAmyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder that has no cure. The underlying mechanistic details of sex differences in the ALS spinal cord, the site of disease onset, are not understood to an extent that could guide novel drug development. To address this, the spinal cords of 120-day-old wild-type (WT) and SOD1G93A (familial mouse model of ALS with mutant superoxide dismutase 1) mice were subjected to untargeted, quantitative proteomics using tandem mass tag acquisition on high-resolution mass spectrometric instrumentation. Compared to WT, both male and female SOD1G93A spinal cords exhibited an upregulation of neuroinflammatory cascades of both peripheral and central origins, as well as a downregulation of proteins reflective of death and dysfunction of cells within the spinal cord. However, female and male SOD1G93A mouse spinal cords exhibited sex-specific differences in proteins compared to respective WT that related to immune response, as well as cellular structure, function, and homeostasis. The proteomic datasets presented provide entire cohort and sex-specific spinal cord drug targets and disease biomarkers in the SOD1G93A mouse model of ALS that may guide future drug development and sex selection in preclinical study designs utilizing the SOD1G93A model.PMID:40117341 | DOI:10.1021/acs.jproteome.4c00990

Arch Microbiol. 2025 Mar 21;207(5):98. doi: 10.1007/s00203-025-04265-8.ABSTRACTThe potential of alkaline-tolerant bacteria as cell factories for the production of functional molecules and bulk chemicals has been increasingly recognized owing to in-depth studies of their metabolic pathways and products combined with their tolerance to alkaline environments. To further explore the cell factory potential of alkaline-tolerant bacteria, it is necessary to systematically analyze and explore the genes and metabolites related to alkaline tolerance. Halomonas alkalicola CICC 11012s is currently the strongest alkaliphile of the genus Halomonas, which can grow at pH 12.5. This study aimed to elucidate the molecular mechanisms underlying the response of H. alkalicola CICC 11012s to alkaline stress, using transcriptomic and metabolomic analyses. The expression of 259 genes and 401 metabolites was significantly altered. Important metabolic pathways included nucleotide, amino acid, and carbohydrate metabolism, as well as membrane transport. Furthermore, an integrative pathway analysis revealed that two pathways, glycine, serine, and threonine metabolism and biotin metabolism, were significantly enriched under high-alkaline conditions (pH 11.0). These findings highlight that deletion of the gene cluster tonB-exbB-exbB2-exbD significantly affects the synthesis of L-aspartate, leading to a decrease in the alkaline tolerance of H. alkalicola.PMID:40116894 | DOI:10.1007/s00203-025-04265-8

Environ Sci Technol. 2025 Mar 21. doi: 10.1021/acs.est.4c10724. Online ahead of print.ABSTRACTEnvironmental exposure is one driving factor of chronic kidney disease (CKD), yet the intrinsic molecular mechanisms are largely unexplored. As a persistent chemical, perfluorooctanesulfonate (PFOS) is regulated due to a great potential to induce multiple diseases, including renal fibrosis, a major pathological characteristic of CKD. It is hypothesized that sodium p-perfluorous nonenoxybenzenesulfonate (OBS), a typical alternative to PFOS, may also induce renal fibrosis. We observed distinct renal fibrosis in mice exposed to OBS. Metabolomics analysis showed that Nα-acetyllysine was the primary metabolite biomarker, whose level decreased greatly due to its excessive consumption by lysyloxidase (LOX). This suppressed the miR-140-5p expression, promoting upregulation of fibroblast growth factor 9 (FGF9), which activated the PI3K/Akt signaling pathway through fibroblast growth factor receptor 3 (FGFR3), thereby enhancing proliferation and activation of fibroblasts. Supplement of Nα-acetyllysine upregulated miR-140-5p expression, reduced expressions of FGF9 and FGFR3, and eventually ameliorated OBS-induced renal fibrosis. Similarly, treatment with miR-140-5p agomir and PI3K/Akt signaling pathway inhibitor LY294002 attenuated OBS-induced renal fibrosis. Taken together, OBS caused renal fibrosis through the LOX-Nα-acetyllysine-miR-140-5p-FGF9-FGFR3-PI3K/Akt-Bad-Bcl-2-fibroblast axis. The results of this study reveal a specific molecular axis for OBS to induce renal fibrosis and call for concerns in supervising the application of OBS.PMID:40116701 | DOI:10.1021/acs.est.4c10724

J Agric Food Chem. 2025 Mar 21. doi: 10.1021/acs.jafc.4c12105. Online ahead of print.ABSTRACTThis study elucidated the mechanisms underlying the immunoregulatory and gut-microbiota-modulating effects of Flammulina velutipes residue polysaccharide (FVRP) using cyclophosphamide (CTX)-induced mouse models. FVRP supplementation alleviated CTX-induced intestinal damage and boosted antioxidant enzyme activity and cytokine secretion. Additionally, FVRP enhanced the diversity and total species richness of the gut microbiota, promoting the proliferation of beneficial bacteria (e.g., Prevotellaceae), while reducing the abundance of CTX-derived bacteria (Lachnospiraceae and Rikenellaceae). FVRP facilitates the accumulation of short-chain fatty acids. Untargeted metabolomic analyses of cecal content revealed that FVRP treatment notably restored the levels of 32 endogenous metabolites altered by CTX. Based on a pseudosterility mice model, fecal microbiota transplantation (FMT), and fecal filtrate transplantation (FFT), gut microbiota and associated metabolites were demonstrated to play a crucial role in the immunomodulatory and protective effects of FVRP against intestinal injury. In conclusion, FVRP exhibits significant potential as an immune enhancer and natural therapeutic agent for alleviating intestinal inflammatory conditions.PMID:40116376 | DOI:10.1021/acs.jafc.4c12105

J Sci Food Agric. 2025 Mar 21. doi: 10.1002/jsfa.14236. Online ahead of print.ABSTRACTBACKGROUND: Lacticaseibacillus paracasei, widely recognized for its safety, is frequently used as a starter culture in fermented foods. In the present study, the differences in the physicochemical properties, antioxidant activities, volatile compounds and non-volatile compounds of mango juice fermented with L. paracasei FJG2339 were evaluated.RESULTS: The results displayed that L. paracasei FJG2339 significantly reduced the total sugar content of mango juice, but slightly increased the contents of polyphenols and flavonoids. Meanwhile, the ABTS [i.e. 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)], DPPH (i.e. 2,2-diphenyl-1-picrylhydrazyl) and OH radical scavenging abilities of mango juice were increased by 28%, 29% and 48%, respectively, after L. paracasei FJG2339 fermentation. Flavor profiles analysis suggested that L. paracasei FJG2339 facilitated the production of acids, alcohols and esters in mango juice, which endow it with a distinct aroma. Untargeted metabolomics analysis displayed that L. paracasei FJG2339 fermentation significantly shifted 207 non-volatile compounds (containing 123 up-regulated non-volatile substances and 84 down-regulated non-volatile substances) of mango juice, which are mainly involved in animo acid metabolism (such as alanine, aspartate and glutamate metabolism, tyrosine metabolism, tryptophan metabolism, phenylalanine metabolism, phenylalanine, and tyrosine and tryptophan biosynthesis).CONCLUSION: These results indicate that L. paracasei FJG2339 fermentation enhances the physicochemical properties, antioxidant capacity and metabolic profiles of mango juices. This study has important implications for the application of fermentation technology of fruit juices. © 2025 Society of Chemical Industry.PMID:40116166 | DOI:10.1002/jsfa.14236

Mol Med Rep. 2025 May;31(5):130. doi: 10.3892/mmr.2025.13495. Epub 2025 Mar 21.ABSTRACTThe application of multi‑omics methodologies, encompassing genomics, transcriptomics, proteomics, metabolomics and integrative genomics, has markedly enhanced the understanding of prostate cancer (PCa). These methods have facilitated the identification of molecular pathways and biomarkers crucial for the early detection, prognostic evaluation and personalized treatment of PCa. Studies using multi‑omics technologies have elucidated how alterations in gene expression and protein interactions contribute to PCa progression and treatment resistance. Furthermore, the integration of multi‑omics data has been used in the identification of novel therapeutic targets and the development of innovative treatment modalities, such as precision medicine. The evolving landscape of multi‑omics research holds promise for not only deepening the understanding of PCa biology but also for fostering the development of more effective and tailored therapeutic interventions, ultimately improving patient outcomes. The present review aims to synthesize current findings from multi‑omics studies associated with PCa and to assess their implications for the improvement of patient management and therapeutic outcomes. The insights provided may guide future research directions and clinical practices in the fight against PCa.PMID:40116118 | DOI:10.3892/mmr.2025.13495

Environ Toxicol Chem. 2025 Mar 20:vgaf080. doi: 10.1093/etojnl/vgaf080. Online ahead of print.NO ABSTRACTPMID:40116074 | DOI:10.1093/etojnl/vgaf080

Plant Biotechnol (Tokyo). 2024 Sep 25;41(3):309-314. doi: 10.5511/plantbiotechnology.24.0719a.ABSTRACTCallus cultures are fundamental for plant propagation, genetic transformation, and emerging biotechnological applications that use cellular factories to produce high-value metabolites like plant-based drugs. These applications exploit the diverse metabolic capabilities of various plant species. However, optimizing culture conditions for specific applications necessitates a deep understanding of the transcriptome, metabolome, and phytohormone profiles of different species. Comprehensive comparative studies of callus characteristics across species are limited. Here, we analyzed the transcriptome, metabolome, and phytohormone profiles of callus cultures from tobacco (Nicotiana tabacum), rice (Oryza sativa), and two bamboo species (Phyllostachys nigra and P. bambusoides). Multivariate analyses of metabolome data revealed similar metabolic trends in these diverse callus cultures and identified metabolites that differ between species. Hormone profiling showed distinct species-specific patterns and notable cytokinin diversity, even between the bamboo species. Moreover, a comparative analysis of 8,256 pairs of syntenic genes between rice and bamboo revealed that 84.7% of these orthologs showed differential expression, indicating significant transcriptomic diversity despite phylogenomic relatedness. Transcriptional regulation of developing organs often involves conserved gene expression patterns across species; however, our findings suggest that callus formation may relax evolutionary constraints on these regulatory programs. These results illustrate the molecular diversity in callus cultures from multiple plant species, emphasizing the need to map this variability comprehensively to fully exploit the biotechnological potential of plant callus cultures.PMID:40115769 | PMC:PMC11921129 | DOI:10.5511/plantbiotechnology.24.0719a

Comput Struct Biotechnol J. 2025 Feb 27;27:869-878. doi: 10.1016/j.csbj.2025.02.033. eCollection 2025.ABSTRACTEuglena gracilis, an algae-derived source of β-glucan, exhibits prebiotic activity that enhances colostrum quality and improves growth, though the underlying mechanisms remain unclear. This study investigates the effects of E. gracilis supplementation during late gestation and lactation on sow colostrum and milk biomolecular profiles. Sixty-one crossbred sows (Landrace × Yorkshire) were assigned to a standard diet (CON; n = 30) or the CON diet supplemented with 1 g/sow/day of E. gracilis (TRT; n = 31) from day 85 of gestation until day 21 of lactation. Sow performance, including litter size and weight, was recorded from birth to day 21 of age. Colostrum samples (n = 20; 10 sows/group) were collected within 1 h of farrowing, and milk samples were collected from the same sows on days 3 and 10 of lactation to assess alterations in non-volatile polar metabolites (NVM), fatty acids (FA), and associated metabolic pathways. On average, the litter size at birth was 14.2 ± 2.5 piglets/litter, with no effect of dietary treatment from birth to day 21 of lactation (P > 0.05). However, piglets suckled by TRT sows tended to have higher average daily gain from birth to day 21 of age than those suckled CON sows (191.0 ± 6.7 vs. 173.6 ± 6.8 g/day, P = 0.073). Chemometric analysis revealed distinct NVM and FA profiles between the groups, particularly in the colostrum. Although E. gracilis supplementation influenced the contents of multiple metabolites, focus has been given to those that have direct impact on piglet development, including increased colostrum leucine (P = 0.001), threonine (P < 0.001), and N-acetylglucosamine (P = 0.002), enhancing colostrum quality and immunomodulatory potential. Elevated colostrum gamma-linolenic acid (P = 0.047) and arachidonic acid (P = 0.019) levels suggested enhanced immune development. Pathways associated with amino sugars and nucleotide sugars and glucose-related metabolism in colostrum were also modulated. These findings suggest E. gracilis-derived β-glucan as a potential dietary supplement for enhancing sow colostrum quality and piglet growth.PMID:40115536 | PMC:PMC11925092 | DOI:10.1016/j.csbj.2025.02.033