PubMed

Ecotoxicol Environ Saf. 2025 Feb 19;292:117932. doi: 10.1016/j.ecoenv.2025.117932. Online ahead of print.ABSTRACTTea plants (Camellia sinensis) tend to accumulate excessive amounts of fluoride (F) compared to other plants. However, the specific mechanisms of F tolerance or detoxification in tea plants remain insufficiently understood. This study employed ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) to identify critical metabolites involved in F detoxification across two distinct tea plant cultivars with varying F accumulation capacities. Notably, malic acid and citric acid emerged as key metabolites that differentially accumulated under F-stressed conditions. Weighted gene co-expression network analysis indicated that C. sinensis aluminum (Al)-activated malate transporter genes CsALMT9 and CsALMT14 may be implicated in the response to F stress in C. sinensis. Further investigations revealed that CsALMT14 localized to the plasma membrane and exhibited significant transcriptional induction upon exposure to F toxicity. Moreover, heterologous expression of CsALMT14 enhanced F tolerance by mitigating F accumulation in transgenic yeast and Arabidopsis thaliana. Additionally, silencing of CsALMT14 by antisense oligodeoxynucleotide and virus-induced gene silencing reduced the content of malic acid but increased the accumulation of citric acid in tea plants, which might be attributed to the down-regulated expression of malic acid synthesis- and citric acid degradation-related genes. These findings suggest that CsALMT14 confers tolerance to F toxicity through F efflux and regulation of malic acid and citric acid metabolism-related gene expression, thereby providing a novel strategy for F detoxification in tea plants.PMID:39978103 | DOI:10.1016/j.ecoenv.2025.117932

Ecotoxicol Environ Saf. 2025 Feb 19;292:117891. doi: 10.1016/j.ecoenv.2025.117891. Online ahead of print.ABSTRACTThe placenta is an important organ for fetal growth. Air pollution during pregnancy may cause adverse effects on offsprings via placental dysfunction. However, the metabolites underlie the effects of PM2.5 on placenta have not been well studied. 329 pregnant women were randomly selected from the Shanghai Maternal-Child Pairs Cohort. Gestational PM2.5 exposure levels were assessed using individual air sampling method and satellite-based exposure assessment mode, respectively. Placental weight, length, width and thickness were measured by obstetrician-gynecologist at the time of delivery. Ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites in serum from the first and third trimester. Associations between PM2.5 and placental characteristics were analyzed by generalized estimating equation and multiple linear regression. The exposure-response relationship was plotted using restricted cubic splines (RCS). Based on the meet-in-the-middle approach, the metabolites underlying the effects of PM2.5 on placenta were explored. The associations between placental width (βTrimester2=-0.497, 95 %CI: -0.801, -0.193), (βTrimester3=-0.279, 95 % CI: -0.543, -0.016) and chorionic disk area (βTrimester2=-12.634,95 %CI: -21.698, -3.570), (βTrimester3=-9.113, 95 %CI: -17.113, -1.112) with PM2.5 exposure at the second and third trimester were found. The associations between placental characteristics with PM2.5 exposure assessed by individual air sampling and satellite-based methods were consistent. L-arginine (L-Arg), caprylic acid (CA), tauroursodeoxycholic acid (TUDCA), glycylproline (Gly-Pro), maltotriose (MT) and N-acetylneuramic acid (NANA) intermediate the effect of PM2.5 exposure on placental chorionic disk area in the third trimester. CONCLUSION: The second and third trimesters may be the sensitive windows of placental abnormalities to PM2.5 exposure. Caprylic acid (CA), glycylproline (Gly-Pro), and N-acetylneuramic acid (NANA) play a key role on the effects of PM2.5 exposure on placenta. This study provides potential biomarkers of placental exposure to PM2.5, providing an opportunity for future research as well as detection.PMID:39978100 | DOI:10.1016/j.ecoenv.2025.117891

Food Chem. 2025 Feb 17;476:143431. doi: 10.1016/j.foodchem.2025.143431. Online ahead of print.ABSTRACTLactiplantibacillus plantarum has been well acknowledged to produce exopolysaccharides (EPS) as a defense mechanism against acid stress. However, the complete biosynthetic pathway of EPS in L. plantarum and its impact on the cell growth and primary metabolism were still unclear. To fill these gaps, we carried out phenotypic, proteomic and metabolomics analysis of L. plantarum HMX2 cultured under different acidic conditions. Component and structure analysis showed that the repeating unit of EPS consisted of N-acetylmannosamine, N-acetylglucosamine, galactose, mannoses and glucoses. Multiomics analysis facilitated the curation and entablement of the complete EPS biosynthetic pathway ready for use in genome-scale metabolic models. Furthermore, proteomics and metabolomics data indicated that compared to the pH 6.5 condition, the acid stress at pH 4.5 significantly accelerated glycolysis and EPS biosynthesis processes while reduced the metabolic fluxes through the TCA cycle and the lactic acid fermentation, which suggested a trade-off between primary and secondary metabolism.PMID:39977986 | DOI:10.1016/j.foodchem.2025.143431

Food Chem. 2025 Feb 6;476:143238. doi: 10.1016/j.foodchem.2025.143238. Online ahead of print.ABSTRACTSeabuckthorn fruit oil (SBFO) is recognized for its high nutritional value, yet it remains highly prone to oxidation during storage. The changes in its primary components and micronutrient molecules during storage have not been thoroughly investigated. This study employed untargeted lipidomics and metabolomics to dynamically monitor alterations in lipid composition and metabolites of SBFO over 30 days of accelerated storage. Lipidomics analysis revealed an increase in TGs and oxidized fatty acids, while sphingolipids, glycerophospholipids, and total lipid content showed significant reductions (p < 0.05). After 30 days, metabolomics combined with bioinformatics analysis identified 13 critical pathways, with linoleic acid metabolism consistently associated with SBFO oxidation. Key oxidation products included 9(S)-HpODE, 9,10,13-TriHOME, and 9,10-DHOME. This study provides potential targets for developing endogenous antioxidants in SBFO and offers new perspectives on the oxidation mechanisms of edible oils.PMID:39977978 | DOI:10.1016/j.foodchem.2025.143238

Hum Reprod Update. 2025 Feb 20:dmaf002. doi: 10.1093/humupd/dmaf002. Online ahead of print.ABSTRACTBACKGROUND: Ovarian aging occurs earlier than the aging of many other organs and has a lasting impact on women's overall health and well-being. However, effective interventions to slow ovarian aging remain limited, primarily due to an incomplete understanding of the underlying molecular mechanisms and drug targets. Recent advances in omics data resources, combined with innovative computational tools, are offering deeper insight into the molecular complexities of ovarian aging, paving the way for new opportunities in drug discovery and development.OBJECTIVE AND RATIONALE: This review aims to synthesize the expanding multi-omics data, spanning genome, transcriptome, proteome, metabolome, and microbiome, related to ovarian aging, from both tissue-level and single-cell perspectives. We will specially explore how the analysis of these emerging omics datasets can be leveraged to identify novel drug targets and guide therapeutic strategies for slowing and reversing ovarian aging.SEARCH METHODS: We conducted a comprehensive literature search in the PubMed database using a range of relevant keywords: ovarian aging, age at natural menopause, premature ovarian insufficiency (POI), diminished ovarian reserve (DOR), genomics, transcriptomics, epigenomics, DNA methylation, RNA modification, histone modification, proteomics, metabolomics, lipidomics, microbiome, single-cell, genome-wide association studies (GWAS), whole-exome sequencing, phenome-wide association studies (PheWAS), Mendelian randomization (MR), epigenetic target, drug target, machine learning, artificial intelligence (AI), deep learning, and multi-omics. The search was restricted to English-language articles published up to September 2024.OUTCOMES: Multi-omics studies have uncovered key mechanisms driving ovarian aging, including DNA damage and repair deficiencies, inflammatory and immune responses, mitochondrial dysfunction, and cell death. By integrating multi-omics data, researchers can identify critical regulatory factors and mechanisms across various biological levels, leading to the discovery of potential drug targets. Notable examples include genetic targets such as BRCA2 and TERT, epigenetic targets like Tet and FTO, metabolic targets such as sirtuins and CD38+, protein targets like BIN2 and PDGF-BB, and transcription factors such as FOXP1.WIDER IMPLICATIONS: The advent of cutting-edge omics technologies, especially single-cell technologies and spatial transcriptomics, has provided valuable insights for guiding treatment decisions and has become a powerful tool in drug discovery aimed at mitigating or reversing ovarian aging. As technology advances, the integration of single-cell multi-omics data with AI models holds the potential to more accurately predict candidate drug targets. This convergence offers promising new avenues for personalized medicine and precision therapies, paving the way for tailored interventions in ovarian aging.REGISTRATION NUMBER: Not applicable.PMID:39977580 | DOI:10.1093/humupd/dmaf002

Bioinformatics. 2025 Feb 20:btaf081. doi: 10.1093/bioinformatics/btaf081. Online ahead of print.ABSTRACTMOTIVATION: Untargeted metabolomics involves a large-scale comparison of the fragmentation pattern of a mass spectrum against a database containing known spectra. Given the number of comparisons involved, this step can be time-consuming.RESULTS: In this work, we present a GPU-accelerated cosine similarity implementation for Tandem Mass Spectrometry (MS), with an approximately 1000-fold speedup compared to the MatchMS reference implementation, without any loss of accuracy. This improvement enables repository-scale spectral library matching for compound identification without the need for large compute clusters. This impact extends to any spectral comparison-based methods such as molecular networking approaches and analogue search.AVAILABILITY: All code, results, and notebooks supporting are freely available under the MIT license at https://github.com/pangeAI/simms/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.PMID:39977359 | DOI:10.1093/bioinformatics/btaf081

Geroscience. 2025 Feb 20. doi: 10.1007/s11357-025-01559-z. Online ahead of print.ABSTRACTThere is growing evidence that higher intermuscular fat (IMF) is associated with worse processing speed, measured by the digit symbol substitution test (DSST) in older adults. However, the underlying biological mechanisms are not well understood. Considering that both muscle and the brain are metabolically active organs, we sought to identify metabolites that may explain the IMF-DSST association. We assessed 613 plasma metabolites in 2388 participants from the Health, Aging, and Body Composition Study (mean age ± SD 74.7 ± 2.9 years, 50% men, 63% white), using liquid chromatography-mass spectrometry. We confirmed that higher IMF was associated with worse DSST scores (standardized beta (95% CI) - 0.08 (- 0.12, - 0.03), p < 0.001). Sixty-six metabolites were significantly associated with both IMF and DSST. Four of the 66 metabolites attenuated the association by ≥ 10%: higher levels of adrenic acid (polyunsaturated fatty acid), and lower levels of C20:5 lysophosphatidylcholine (lysophospholipid), 1-methylnicotinamide (vitamin B3-related myokine), and maslinic acid (triterpene) were associated with higher IMF and worse DSST. Together, they explained 41% of the IMF-DSST association. Pathway enrichment analyses identified two significant shared pathways: unsaturated fatty acid metabolism and the citrate (TCA) cycle. This study provides hypothesis-generating evidence that a set of circulating metabolites related to unsaturated fatty acids, energy metabolism, and myokines may partially explain the inverse association of IMF with processing speed. The findings, if further confirmed by independent studies, advance our understanding of molecular pathways underlying muscle-brain crosstalk. Whether the identified metabolites are early predictors of future decline in processing speed should be further investigated.PMID:39976843 | DOI:10.1007/s11357-025-01559-z

Nat Prod Rep. 2025 Feb 20. doi: 10.1039/d4np00064a. Online ahead of print.ABSTRACTCovering: 1982 up to the end of 2024Marine exometabolites (EMs) are small molecules released by marine (micro)organisms into the seawater. Collectively, all of the released EMs contribute to the chemical seascape of a marine ecosystem. Accessing and describing these waterborne molecules are a key focus of various disciplinary fields that aim to study marine biogeochemical cycles, translate the chemical language of the oceans (chemical ecology), or discover new structural entities with biological properties (natural product discovery). Beginning with the semantics of marine exometabolites, this review elucidates the different sampling methods and MS-based metabolomic analyses that are used to describe the chemical composition of seawater of benthic ecosystems. These technical and analytical advances offer promising avenues for describing the structural diversity of marine exometabolites and deciphering their functions in various ecological contexts.PMID:39976689 | DOI:10.1039/d4np00064a

Anal Bioanal Chem. 2025 Feb 20. doi: 10.1007/s00216-025-05785-4. Online ahead of print.ABSTRACTThe spatial metabolic analysis of tumor tissues following neoadjuvant chemotherapy (NAC) is critical for understanding chemotherapy-induced metabolic changes. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) offers a powerful tool for revealing spatially resolved metabolic profiles within tissues. However, necrotic regions in post-NAC tissues are fragile, creating challenges for sample preparation and MALDI MSI analysis. In this study, we introduce an optimized workflow employing conductive tape to stabilize tissue samples during sectioning and MALDI MSI analysis, preserving necrotic areas while maintaining tissue integrity. Using this technique, we successfully mapped metabolic alterations across necrotic and viable regions of post-NAC tumor tissues, providing new insights into metabolic changes that occur after chemotherapy. Our findings establish MALDI MSI as a valuable tool for spatially resolved metabolomics in post-NAC tumor tissues, offering insights into chemotherapy-induced metabolic changes.PMID:39976685 | DOI:10.1007/s00216-025-05785-4

J Virol. 2025 Feb 20:e0228224. doi: 10.1128/jvi.02282-24. Online ahead of print.ABSTRACTCoronaviruses hijack host cell metabolic pathways and resources to support their replication. They induce extensive host endomembrane remodeling to generate viral replication organelles and exploit host membranes for assembly and budding of their enveloped progeny virions. Because of the overall significance of host membranes, we sought to gain insight into the role of host factors involved in lipid metabolism in cells infected with Middle East respiratory syndrome coronavirus (MERS-CoV). We employed a single-cycle infection approach in combination with pharmacological inhibitors, biochemical assays, lipidomics, and light and electron microscopy. Pharmacological inhibition of acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN), key host factors in de novo fatty acid biosynthesis, led to pronounced inhibition of MERS-CoV particle release. Inhibition of ACC led to a profound metabolic switch in Huh7 cells, altering their lipidomic profile and inducing lipolysis. However, despite the extensive changes induced by the ACC inhibitor, the biogenesis of viral replication organelles remained unaffected. Instead, ACC inhibition appeared to affect the trafficking and post-translational modifications of the MERS-CoV envelope proteins. Electron microscopy revealed an accumulation of nucleocapsids in early budding stages, indicating that MERS-CoV assembly is adversely impacted by ACC inhibition. Notably, inhibition of palmitoylation resulted in similar effects, while supplementation of exogenous palmitic acid reversed the compound's inhibitory effects, possibly reflecting a crucial need for palmitoylation of the MERS-CoV spike and envelope proteins for their role in virus particle assembly.IMPORTANCEMiddle East respiratory syndrome coronavirus (MERS-CoV) is the etiological agent of a zoonotic respiratory disease of limited transmissibility between humans. However, MERS-CoV is still considered a high-priority pathogen and is closely monitored by WHO due to its high lethality rate of around 35% of laboratory-confirmed infections. Like other positive-strand RNA viruses, MERS-CoV relies on the host cell's endomembranes to support various stages of its replication cycle. However, in spite of this general reliance of MERS-CoV replication on host cell lipid metabolism, mechanistic insights are still very limited. In our study, we show that pharmacological inhibition of acetyl-CoA carboxylase (ACC), a key enzyme in the host cell's fatty acid biosynthesis pathway, significantly disrupts MERS-CoV particle assembly without exerting a negative effect on the biogenesis of viral replication organelles. Furthermore, our study highlights the potential of ACC as a target for the development of host-directed antiviral therapeutics against coronaviruses.PMID:39976449 | DOI:10.1128/jvi.02282-24

Appl Environ Microbiol. 2025 Feb 20:e0237624. doi: 10.1128/aem.02376-24. Online ahead of print.ABSTRACTThe purpose of this study was to evaluate the combined effects of puerarin (Pue) and insoluble dietary fiber from Hericium erinaceus (HEIDF) on obesity induced by a high-fat diet (HFD) in mice, focusing on their effects on lipid and glucose metabolism, gut microbiota (GM), and serum metabolites. Glucose tolerance, tissue pathology, and serum biochemical levels were conducted to assess the effects of puerarin combined with Hericium Erinaceus insoluble dietary fiber (LH) on glucose and lipid metabolism. 16S rRNA sequencing and untargeted metabonomics were employed to explore the underlying mechanisms. The results showed that the LH group significantly reduced body weight and hepatic and adipose lipid accumulation, and improved glucose tolerance and dyslipidemia compared to the Pue or HEIDF groups alone. Moreover, the LH group exhibited enhanced regulation of GM, including increased microbial diversity, higher abundance of beneficial bacteria such as g__Lactobacillus and g__Bacillus, and a decreased Firmicutes-to-Bacteroidota ratio. In addition, the LH group ameliorated HFD-induced serum metabolite changes and promoted the activation of tryptophan and glycerophospholipid metabolism pathways. The combination of Pue and HEIDF exhibits a synergistic anti-obesity effect by modulating specific GM (g__Lactobacillus and g__Bacillus) and serum metabolites.IMPORTANCEThe combination of HEIDF and Pue holds significant importance in the context of obesity. This synergistic effect not only aids in weight management but may also enhance metabolic health through various mechanisms, including increased satiety and promotion of fat oxidation. Therefore, incorporating these two components into the daily diet could offer effective strategies for the prevention and intervention of obesity and its related diseases.PMID:39976439 | DOI:10.1128/aem.02376-24

Ann Neurol. 2025 Feb 20. doi: 10.1002/ana.27208. Online ahead of print.ABSTRACTOBJECTIVE: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by altered metabolome and energy homeostasis, manifesting with body mass index changes and hypermetabolism-both prognostic of disease progression and survival. The cross-sectional ALS metabolome has been characterized, but longitudinal correlations to functional decline are lacking.METHODS: We longitudinally evaluated metabolomes from ALS plasma and terminal postmortem spinal cord and brain motor cortex tissue. We constructed 3 plasma models. A linear mixed effects model correlated all metabolite levels across all timepoints to their corresponding functional scores. An interaction model predicted a longitudinal change in function from baseline metabolites, whereas a progression model identified metabolites linked to a 20% or 50% drop in function. In postmortem samples, differential metabolites in onset versus second spinal cord segments served as a surrogate of disease progression. Mendelian randomization assessed potential causality from metabolites.RESULTS: In plasma, all models primarily selected lipid metabolites and sub-pathways, in addition to amino acids, xenobiotics, and various less frequently selected pathways. Among lipids, fatty acids and sphingomyelins were predominant, along with plasmalogens, phosphatidylcholines, and lysophospholipids. Sex interaction findings were nominal. In the spinal cord, sphingomyelin and long-chain saturated and monounsaturated fatty acids were more abundant in the onset segment tissue, whereas phosphatidylcholines and phosphatidylethanolamines were less abundant. Mendelian randomization suggested that impaired carnitine and short chain acylcarnitine metabolism may be genetically determined in ALS, along with various antioxidant derivatives.INTERPRETATION: Our findings suggest metabolomic changes primarily involving different lipid classes and carnitine metabolism may underscore ALS severity and progression. ANN NEUROL 2025.PMID:39976286 | DOI:10.1002/ana.27208

Psychol Med. 2025 Feb 20;55:e57. doi: 10.1017/S0033291725000339.NO ABSTRACTPMID:39976211 | DOI:10.1017/S0033291725000339

Front Immunol. 2025 Feb 5;16:1502605. doi: 10.3389/fimmu.2025.1502605. eCollection 2025.ABSTRACTUlcerative colitis is a chronic disease that has not well-established etiology. The role of microbial dysregulation in its pathogenesis has been recently highlighted. Overall, microbiome alterations concern the reduction of bacterial abundance and diversity, resulting in gut microbiome imbalance negatively affecting immunological aspects. There is a link between ulcerative colitis and the oral microbiome. The changes of oral microbiome are found at many levels, from gently dysbiotic composition to the presence of the main periodontal microbes. The analysis of oral microbiome can be a part of personalized medicine due to the fact that it is a potential biomarker. Patients with ulcerative colitis may manifest dental symptoms/problems, such as periodontitis (strongly related to the red-complex pathogens-Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and bacteria belonging to the other complexes, such as Fusobacterium nucleatum and Aggregatibacter actinomycetecomitans), dental caries, oral ulcerations, leukoplakia, halitosis, and others. Notably, the DMFT (Decayed, Missing, Filled Teeth) index is higher in these patients compared to healthy subjects. According to some data, oral lichen planus (which is a disease with an immunological background) can also be observed in ulcerative colitis patients. It seems that deep understanding of ulcerative colitis in association with oral microbiome, immunology, and dental manifestations may be crucial to provide complex treatment from a dental point of view.PMID:39975550 | PMC:PMC11836005 | DOI:10.3389/fimmu.2025.1502605

bioRxiv [Preprint]. 2025 Feb 5:2025.02.04.636472. doi: 10.1101/2025.02.04.636472.ABSTRACTThe "dark matter" of metabolomics refers to the large number of unidentified features in metabolomic studies, mostly from mass spectrometry (MS) based analysis (deSilva2015; David2021; Giera2024). The topic is pertinent to the analytical coverage of small molecules in biomedical research (Kind2009; Uppal2016), approaches to metabolite annotation (Domingo2018; Chaleckis2019; Metz2025), mapping reaction pathways (Zamboni2015) and the promise of applying metabolomics and exposomics to precision medicine (Wishart2016; Vermeulen2020). The number of unidentified features is not a direct account of number of compounds, as a metabolite can have isotopologues, adducts and fragments that are measured in the same data (Mahieu2017; Wang2019; Li2023a). Giera et al (2024) recently reported that in-source fragments (ISFs) accounted for over 70% of MS/MS features in METLIN, one of the leading spectral databases, suggesting that ISFs could be a significant portion of the "dark matter". Since the reference spectra in METLIN are based on chemical standards, we examine here the LC-MS (liquid chromatography coupled mass spectrometry) metabolomics from biological samples, which are the most relevant in biomedical investigations.PMID:39975275 | PMC:PMC11838597 | DOI:10.1101/2025.02.04.636472

bioRxiv [Preprint]. 2025 Feb 8:2025.02.03.636312. doi: 10.1101/2025.02.03.636312.ABSTRACTNeutrophils are highly abundant innate immune cells that are constantly produced from myeloid progenitors in the bone marrow. Differentiated neutrophils can perform an arsenal of effector functions critical for host defense. This study aims to quantitatively understand neutrophil mitochondrial metabolism throughout differentiation and activation, and to elucidate the impact of mitochondrial metabolism on neutrophil functions. To study metabolic remodeling throughout neutrophil differentiation, murine ER-Hoxb8 myeloid progenitor-derived neutrophils and human induced pluripotent stem cell-derived neutrophils were assessed as models. To study the metabolic remodeling upon neutrophil activation, differentiated ER-Hoxb8 neutrophils and primary human neutrophils were activated with various stimuli, including ionomycin, MSU crystals, and PMA. Characterization of cellular metabolism by isotopic tracing, extracellular flux analysis, metabolomics, and fluorescence-lifetime imaging microscopy revealed dynamic changes in mitochondrial metabolism. As neutrophils mature, mitochondrial metabolism decreases drastically, energy production is fully offloaded from oxidative phosphorylation, and glucose oxidation through TCA cycle is substantially reduced. Nonetheless, mature neutrophils retain the capacity for mitochondrial metabolism. Upon stimulation with certain stimuli, TCA cycle is rapidly activated. Mitochondrial pyruvate carrier inhibitors reduce this re-activation of the TCA cycle and inhibit the release of neutrophil extracellular traps. Mitochondrial metabolism also impacts neutrophil redox status, migration, and apoptosis without significantly changing overall bioenergetics. Together, these results demonstrate that mitochondrial metabolism is dynamically remodeled and plays a significant role in neutrophil function and fate. Furthermore, these findings point to the therapeutic potential of mitochondrial pyruvate carrier inhibitors in a range of conditions where dysregulated neutrophil response drives inflammation and contributes to pathology.PMID:39975244 | PMC:PMC11838513 | DOI:10.1101/2025.02.03.636312

bioRxiv [Preprint]. 2025 Feb 7:2024.09.30.615873. doi: 10.1101/2024.09.30.615873.ABSTRACTJoint injury is a risk factor for post-traumatic osteoarthritis. However, metabolic and microarchitectural changes within the joint post-injury in both sexes remain unexplored. This study identified tissue-specific and spatially-dependent metabolic signatures in male and female mice using matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) and LC-MS metabolomics. Male and female C57Bl/6J mice were subjected to non-invasive joint injury. Eight days post-injury, serum, synovial fluid, and whole joints were collected for metabolomics. Analyses compared between injured, contralateral, and naïve mice, revealing local and systemic responses. Data indicate sex influences metabolic profiles across all tissues, particularly amino acid, purine, and pyrimidine metabolism. MALDI-MSI generated 2D ion images of bone, the joint interface, and bone marrow, highlighting increased lipid species in injured limbs, suggesting physiological changes across injured joints at metabolic and spatial levels. Together, these findings reveal significant metabolic changes after injury, with notable sex differences.SIGNIFICANCE STATEMENT: Osteoarthritis, the leading cause of disability worldwide, disproportionately affects females with sex being one of the strongest predictors of disease. This disparity is partly driven by sex-specific differences in injury susceptibility, increasing the likelihood of traumatic injury to the anterior cruciate ligament (ACL), other ligaments, and menisci. Using a non-invasive injury model, we demonstrate that injury perturbs the local joint environment and has systemic effects in a sex-specific manner. Furthermore, by leveraging matrix-assisted laser desorption ionization-mass spectrometry imaging of the joint, we provide new insight into the composition of osteochondral tissue at the metabolite level. These sexually dimorphic metabolic responses to joint injury advance current understanding of the complex sexual dimorphism in OA pathogenesis providing a foundation for targeted therapeutic strategies and improved patient outcomes for female patients.PMID:39975211 | PMC:PMC11838485 | DOI:10.1101/2024.09.30.615873

bioRxiv [Preprint]. 2025 Feb 8:2025.02.05.636747. doi: 10.1101/2025.02.05.636747.ABSTRACTBACKGROUND: The rumen harbors a diverse and dynamic microbiome vital in digesting vegetation into metabolic byproducts for energy and general biological function. Although previous studies have reported connections between the rumen and the overall health of the sheep, the exact biological process by which this occurs is not well understood. Therefore, our study aimed to quantify sheep rumen metabolites to determine if enriched biological pathways are differentiable across phenotypic features of sex, age, and weight.RESULTS: We collected and quantified metabolites of rumen samples from sixteen sheep using liquid chromatography-tandem mass spectrometry. We performed a series of univariate and multivariate statistical analyses to interpret the rumen metabolomics data. To identify metabolic pathways associated with the phenotypic features of sex, weight, and age, we used MetaboAnalyst, which identified amino acid metabolism as a distinguishing factor. Among the pathways, phenylalanine metabolism emerged as a key pathway differentiating sheep based on sex and age. Additionally, phenylalanine, tyrosine, and tryptophan biosynthesis were exclusively associated with age. In univariate linear models, we also discovered that these amino acid and protein pathways were associated with weight by age-corrected effect. Finally, we identified arginine and proline biosynthesis as a pathway linked to metabolites with weight.CONCLUSION: Our study identified differential pathways based on the sex, age, and weight features of sheep. Metabolites produced by the rumen may act as an indicator for sheep health and other ruminants. These findings encourage further investigation of the differentially produced metabolites to assess overall sheep health.PMID:39975146 | PMC:PMC11839056 | DOI:10.1101/2025.02.05.636747

bioRxiv [Preprint]. 2025 Feb 2:2025.01.28.635396. doi: 10.1101/2025.01.28.635396.ABSTRACTMediation analysis helps uncover how exposures impact outcomes through intermediate variables. Traditional mean-based total mediation effect measures can suffer from the cancellation of opposite component-wise effects and existing methods often lack the power to capture weak effects in high-dimensional mediators. Additionally, most existing work has focused on continuous outcomes, with limited attention to binary outcomes, particularly in case-control studies. To fill in this gap, we propose an R 2 total mediation effect measure under the liability framework, providing a causal interpretation and applicable to various high-dimensional mediation models. We develop a cross-fitted, modified Haseman-Elston regression-based estimation procedure tailored for case-control studies, which can also be applied to cohort studies with reduced efficiency. Our estimator remains consistent with non-mediators and weak effect sizes in extensive simulations. Theoretical justification on consistency is provided under mild conditions. In the Women's Health Initiative of 2150 individuals, we found that 89% (CI: 73% 91%) of the variation in the underlying liability for coronary heart disease associated with BMI can be explained by metabolomics.PMID:39975081 | PMC:PMC11838279 | DOI:10.1101/2025.01.28.635396

bioRxiv [Preprint]. 2025 Feb 6:2025.02.05.636675. doi: 10.1101/2025.02.05.636675.ABSTRACTThe recent ICH M12 guidance on Drug Interaction Studies encourages the use of alternate approaches for predicting drug-drug interaction (DDI) potential of new chemical entities. One approach involves biomarkers, which are endogenous substrates of drug metabolizing enzymes and transporters (DMET) and can be used to assess the inhibitory potential of new chemical entities during Phase 1 clinical studies. Thus, biomarkers could potentially eliminate the need for dedicated DDI studies with exogenous probe substrates. Metabolomics, in conjunction with in vitro and/or in vivo preclinical models or clinical studies, can be used for biomarker discovery. We developed and applied a novel metabolomics-based DMET biomarker discovery (MDBD) approach to identify and qualify biomarkers of renal organic anion transporter 1 (OAT1) and OAT3. Untargeted metabolomics of pooled plasma and urine samples from a pharmacokinetic DDI study using the OAT1/3 inhibitor, probenecid, yielded 153 features identified as putative OAT1/3 biomarkers. Subsequently, in vitro transporter uptake assays using processed urine samples confirmed 57 of these features as OAT1 and/or OAT3 substrates. Finally, 23 features were clinically validated as OAT1/3 biomarkers through a detailed pharmacokinetic analysis (0-24 h) of plasma and urine samples. These biomarkers, either alone or as part of a panel, can predict OAT1/3-mediated DDIs and interindividual variability in the renal secretory clearance of organic anions across different populations, thereby enabling translational utility in clinical settings. The novel MDBD approach can be extended to discover biomarkers of other transporters and enzymes.SUMMARY: Using clinical and mechanistic in vitro approaches, 23 endogenous substrates of OAT1/3 were identified as potential clinical biomarkers of renal secretary elimination of organic anions.PMID:39975069 | PMC:PMC11838602 | DOI:10.1101/2025.02.05.636675