Metabolites

18 pages, 1673 KB

Open AccessReview

A Structured Computational Roadmap for Lipidomics in R: Reproducible Workflows from Raw Data to Functional Insight

by Maria-Christina P. Papatheodorou, Panagiotis Vlamos and Marios G. Krokidis

Metabolites 2026, 16(5), 288; https://doi.org/10.3390/metabo16050288 - 22 Apr 2026

Lipidomics has emerged as a transformative discipline in biomedical research, providing high-resolution insights into metabolic signaling and disease pathophysiology. The R programming language provides a widely adopted framework for extensible analysis of complex lipidomic datasets due to its robust biostatistical infrastructure. Herein, we [...] Read more.

Lipidomics has emerged as a transformative discipline in biomedical research, providing high-resolution insights into metabolic signaling and disease pathophysiology. The R programming language provides a widely adopted framework for extensible analysis of complex lipidomic datasets due to its robust biostatistical infrastructure. Herein, we present a comprehensive roadmap for lipidomics in R, structured around a standardized analytical lifecycle: from raw data acquisition and preprocessing to structural annotation, statistical modeling and functional interpretation. We critically contextualize and integrate a curated suite of widely adopted R packages (version 4.3.0), including xcms and MSnbase for feature extraction, LipidMS 3.0 for fragmentation-based identification, and lipidr for quality control and normalization. Furthermore, we demonstrate how advanced tools such as mixOmics and clusterProfiler can be integrated to bridge the gap between differential lipid abundance and systems-level biological insights. Particular emphasis is placed on reproducibility, nomenclature standardization and the emerging role of machine learning in biomarker discovery. By synthesizing these resources into a coherent pipeline, this guide provides a structured reference for researchers. Further discussion addresses methodological pitfalls, statistical assumptions and reproducibility constraints that frequently compromise lipidomics studies. Ultimately, this structured approach facilitates systematic tool selection, accelerating the translation of complex lipidomic signatures into reproducible and clinically meaningful discoveries. Full article

(This article belongs to the Special Issue Lipidomic and Metabolomic Analysis of Neurodegenerative Diseases)

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15 pages, 659 KB

Open AccessReview

Altered Lipid Metabolism in Psoriatic Arthritis: A Comprehensive Review

by Stanislava Popova-Belova, Mariela Geneva-Popova, Stefka Stoilova, Velichka Popova, Georgi Nikolov and Dimitar Nikolov

Metabolites 2026, 16(5), 287; https://doi.org/10.3390/metabo16050287 - 22 Apr 2026

Abstract

Psoriatic arthritis (PsA) is a chronic inflammatory disorder affecting both the joints and skin. Beyond musculoskeletal manifestations, patients with PsA frequently exhibit alterations in lipid metabolism, contributing to an increased risk of cardiovascular disease. Dyslipidemia in PsA arises from multiple mechanisms, including systemic [...] Read more.

Psoriatic arthritis (PsA) is a chronic inflammatory disorder affecting both the joints and skin. Beyond musculoskeletal manifestations, patients with PsA frequently exhibit alterations in lipid metabolism, contributing to an increased risk of cardiovascular disease. Dyslipidemia in PsA arises from multiple mechanisms, including systemic inflammation, insulin resistance, and imbalances in adipokines such as leptin, adiponectin, and resistin. A structured literature search was conducted in PubMed, Scopus, and Web of Science to identify relevant studies on lipid metabolism in psoriatic arthritis, and the evidence was synthesized narratively. PsA is also commonly associated with obesity and metabolic syndrome, further exacerbating dyslipidemia and cardiovascular risk. Interventions including weight loss, lifestyle modification, and anti-inflammatory treatments have been shown to improve lipid profiles and clinical outcomes. This review provides a comprehensive overview of current knowledge on altered lipid metabolism in PsA, highlighting underlying mechanisms, clinical implications, and therapeutic strategies to reduce cardiovascular risk. Full article

(This article belongs to the Special Issue Psoriasis and Metabolic Syndrome)

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17 pages, 2662 KB

Open AccessArticle

Effects of a Reprometabolic Syndrome-Inducing Eucaloric High-Fat Diet on Insulin Sensitivity, Body Composition, the Lipidome, and the Microbiome

by Irene E. Schauer, Katherine Kuhn, Andrew P. Bradford, Angela J. Fought, Daniel N. Frank, Cassandra V. Kotter, Charles E. Robertson, Katie Duffy and Nanette Santoro

Metabolites 2026, 16(5), 286; https://doi.org/10.3390/metabo16050286 - 22 Apr 2026

Abstract

Background: We previously demonstrated recapitulation of the relative hypogonadotropic hypogonadism of obesity, the Reprometabolic Syndrome (RMS), in women of normal BMI with a one-month high-fat, eucaloric diet (HFD). Objective: Assess effects of HFD on sleep, body composition and lifestyle and metabolic [...] Read more.

Background: We previously demonstrated recapitulation of the relative hypogonadotropic hypogonadism of obesity, the Reprometabolic Syndrome (RMS), in women of normal BMI with a one-month high-fat, eucaloric diet (HFD). Objective: Assess effects of HFD on sleep, body composition and lifestyle and metabolic secondary outcomes and correlate insulin sensitivity changes with the RMS. Methods: A total of 18 normally cycling women aged 18–38 with BMI 18–24 kg/m² were enrolled for a four-month study including a eucaloric HFD (48% calories from fat) for one menstrual cycle. Activity, sleep, body composition, and the lipidome were measured in all participants. Fecal microbiome was analyzed in the last nine participants, and insulin sensitivity by two-stage hyperinsulinemic euglycemic clamp was measured before and after HFD in 15 participants. Results: Relative to the pre-diet period, BMI, activity and sleep measures did not change, except for waking after sleep onset (WASO), which appeared to decrease during and post HFD. DXA revealed statistically significant decreases in total percent fat, total fat mass, visceral fat volume, and trunk fat volume. Whole-body insulin sensitivity decreased with the HFD while adipocyte insulin sensitivity was unaffected. Insulin sensitivity changes did not correlate with change in gonadotropins or response to gonadotropin releasing hormone (GnRH). Multiple significant changes in plasma lipids were observed, including increased ceramides and glucosylceramides. Microbiome analysis revealed increased microbial diversity. Conclusions: A one-month eucaloric HFD that induced RMS in normal-weight, reproductive-aged women also induced whole-body insulin resistance (IR) and multiple lipidomics changes potentially associated with IR. These changes in IR occurred despite overall stable activity, BMI and sleep, but did not correlate with the HPO axis defects. The unexpected decrease in body fat and increase in microbial diversity may be related to specific dietary elements of the HFD. Full article

(This article belongs to the Special Issue Effects of Nutrition Intake and Lifestyle Intervention on Human Metabolic Health)

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13 pages, 2946 KB

Open AccessArticle

Aerobic Exercise Alleviates Oxidative Stress and Inflammation to Attenuate High-Fat Diet-Induced Non-Alcoholic Fatty Liver Disease in ApoE^-/- Mice

by Liang Zhang, Wenxin Wang, Fengting Zheng, Jialu Weng, Yao Lu, Qingbo Li, Ting Li, Wei Li and Lifeng Wang

Metabolites 2026, 16(4), 285; https://doi.org/10.3390/metabo16040285 - 21 Apr 2026

Abstract

Background/Objectives: The development of non-alcoholic fatty liver disease (NAFLD) is closely linked to oxidative stress and inflammation. Aerobic exercise has been shown to improve NAFLD, although its underlying mechanisms remain incompletely understood. This study utilized ApoE^-/- mice to investigate the role [...] Read more.

Background/Objectives: The development of non-alcoholic fatty liver disease (NAFLD) is closely linked to oxidative stress and inflammation. Aerobic exercise has been shown to improve NAFLD, although its underlying mechanisms remain incompletely understood. This study utilized ApoE^-/- mice to investigate the role of Sestrin2 in aerobic exercise-induced amelioration of NAFLD. Methods: Random assignment of C57BL/6J and ApoE^-/- mice yielded four groups: C (control), CE (aerobic exercise), AS (ApoE^-/- control), and AE (ApoE^-/- aerobic exercise). Aerobic exercise lasting 12 weeks was administered to the CE and AE groups. Serum biomarkers were analyzed by ELISA, liver tissue morphology was assessed via HE and ORO staining, and macrophage polarization was evaluated through immunofluorescence. Additionally, mRNA and protein expression levels were measured by qPCR and Western blot. Results: Aerobic exercise reduced liver wet weight, lipid accumulation, and steatosis in ApoE^-/- mice. Aerobic exercise attenuates hepatic oxidative stress, and upregulated the expression of regulation oxidative stress related gene and proteins of Nrf2, HO-1, CAT, and SOD1 in ApoE^-/- mice. Aerobic exercise promoted a shift in macrophage polarization from the pro-inflammatory M1 phenotype toward the anti-inflammatory M2 phenotype in the liver, and significantly reduced TNF-α and IL-1β levels, accompanied by upregulation of Sestrin2 expression, enhanced AMPK phosphorylation, inhibited mTORC1 in the liver. Conclusions: These findings suggest that aerobic exercise alleviates oxidative stress and inflammation in NAFLD, with Sestrin2 activation playing a central role. Full article

(This article belongs to the Section Endocrinology and Clinical Metabolic Research)

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16 pages, 7279 KB

Open AccessArticle

Quercetin Attenuates Non-Alcoholic Fatty Liver Disease in Association with the Inhibition of Hepatic IL-1β/iNOS and IL-1β/CD45 Axes of Inflammation and Fibrosis Accompanied by Reduced Endogenous Metabolites and Apoptosis

by Saif A. Alqahtani, Hanan H. Alshehri, Hend Ashour, Hend Abdallah, Laila Rashed, Rehab M. Badi, Muataz E. D. Mohammed, Bahjat Al-Ani, Norah M. Alzamil, Alia Albawardi and Basma E. Aboulhoda

Metabolites 2026, 16(4), 284; https://doi.org/10.3390/metabo16040284 - 21 Apr 2026

Abstract

Background: Liver inflammation and fibrosis are directly associated with non-alcoholic fatty liver disease (NAFLD). Dysregulation of the potent pro-inflammatory cytokine interleukin-1 beta (IL-1β), inducible nitric oxide synthase (iNOS), and tissue leukocyte infiltration (CD45 +ve) are connected with multiorgan injury and fibrosis. We investigated [...] Read more.

Background: Liver inflammation and fibrosis are directly associated with non-alcoholic fatty liver disease (NAFLD). Dysregulation of the potent pro-inflammatory cytokine interleukin-1 beta (IL-1β), inducible nitric oxide synthase (iNOS), and tissue leukocyte infiltration (CD45 +ve) are connected with multiorgan injury and fibrosis. We investigated whether the induction of NAFLD can cause dysregulation in the hepatic IL-1β/iNOS and IL-1β/CD45 axes of inflammation and fibrosis, as well as in endogenous metabolites (lipids, glucose, and insulin) and apoptosis, in the presence and absence of the flavonoid quercetin. Methods: The model group of rats was fed with a high-fat and high-carbohydrate diet (HFCD) for 4 weeks. The protective group of rats was given both quercetin (50 mg/kg) and HFCD for 4 weeks. All rats were sacrificed on day 29. Results: NAFLD was induced in rats as demonstrated by dyslipidemia, hyperglycemia, insulin resistance, liver inflammation, and elevation of liver injury enzymes. NAFLD was also associated with the upregulation of hepatic IL-1β, iNOS, CD45, and apoptosis (p53). Biomarkers of fibrosis (TIMP-1 and α-SMA) were also elevated, and fibrosis was confirmed in the model group by increased collagen deposition and elevated stages of fibrosis score (Stage 1 to 2 of Brunt’s NASH classification). All these parameters were significantly (p < 0.01) modulated by quercetin treatment. Additionally, a significant (p < 0.001) correlation between IL-1β and hepatic injury parameters was observed. Conclusions: These findings suggest a potential association between NAFLD and the IL-1β/iNOS and IL-1β/CD45 axes of liver injury and fibrosis, as well as dyslipidemia, glycemia, and apoptosis, with quercetin exhibiting beneficial hepatic pleiotropic effects. Full article

(This article belongs to the Special Issue Biomarkers in Obesity, Metabolic Syndrome, and Weight Loss: Advances in Diagnosis, Risk Stratification, and Personalized Management)

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13 pages, 703 KB

Open AccessArticle

Comparative Analysis of Two Dietary Saturated Fat Types on Metabolite Profiles Crossing the Blood–Brain Barrier of Poultry Chicks

by Oluteru E. Orimaye, Paul C. Omaliko, Nathanael I. Lichti, Bruce R. Cooper and Yewande O. Fasina

Metabolites 2026, 16(4), 283; https://doi.org/10.3390/metabo16040283 - 20 Apr 2026

Abstract

Background: The dorsal raphe nucleus (DRN) produces and distributes serotonin, while the hypothalamus (HYP) uses serotonergic signals to regulate physiological processes in chickens. Coconut oil (COCO), rich in medium-chain fatty acids, is rapidly absorbed without re-esterification. Methods: Day-old broilers (Ross 708 male, n [...] Read more.

Background: The dorsal raphe nucleus (DRN) produces and distributes serotonin, while the hypothalamus (HYP) uses serotonergic signals to regulate physiological processes in chickens. Coconut oil (COCO), rich in medium-chain fatty acids, is rapidly absorbed without re-esterification. Methods: Day-old broilers (Ross 708 male, n = 160) were distributed into two dietary treatments with five replicates of 16 birds each. The birds were fed a corn–soybean meal (SBM) basal diet supplemented with 3% of poultry fat (CON) or coconut oil (COCO). The body-weight gain (BWG), feed intake (FI), and feed conversion ratio (FCR) were recorded over a 3-week period, and the data were subjected to a t-test. Untargeted metabolomic analysis by high-performance liquid chromatography (HPLC-MS) was used to evaluate the influence of the type of dietary fat on metabolite profiles in the DRN, HYP, and plasma of broiler chickens. Principal component analysis (PCA) was used to identify unique metabolites, and ANOVA was used to identify the metabolites that were significantly abundant (p < 0.05). The metabolites were then annotated using the KEGG and HMDB databases. Results: Birds in the COCO treatment gained more weight on average (0.8446 kg/bird) than birds in the CON group (0.8132 kg/bird; p = 0.0496). Five metabolites associated with multiple significant cellular processes, such as brain function, energy metabolism, and neurotransmission, showed similar differential expression patterns, while two metabolic pathways (butanoate metabolism and alanine, aspartate and glutamate metabolism) were identified. Conclusions: The dietary inclusion of COCO improves BWG in poultry and enhances their overall well-being by modulating metabolite profiles, supporting neurotransmission, and enriching the metabolic pathways essential for growth and brain function. Full article

(This article belongs to the Section Metabolomic Profiling Technology)

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18 pages, 9235 KB

Open AccessArticle

Critical Role for Malic Enzymes in MYC-Mediated Cellular Adaptation to Glutamine Depletion

by Yufan Si, Wei Li, Yang Chen, Jiayang Yuan, Chenrui Hu, Yanan Liu and Li Li

Metabolites 2026, 16(4), 282; https://doi.org/10.3390/metabo16040282 - 20 Apr 2026

Abstract

Background/Objectives: MYC-driven tumors exhibit significant glutamine addiction, but the metabolic adaptation mechanisms enabling their survival under glutamine deprivation remain incompletely understood. Malic enzymes catalyze the oxidative decarboxylation of malate to pyruvate while generating NADPH, linking central carbon metabolism to redox homeostasis. This study [...] Read more.

Background/Objectives: MYC-driven tumors exhibit significant glutamine addiction, but the metabolic adaptation mechanisms enabling their survival under glutamine deprivation remain incompletely understood. Malic enzymes catalyze the oxidative decarboxylation of malate to pyruvate while generating NADPH, linking central carbon metabolism to redox homeostasis. This study investigates whether and how ME1 and ME2 mediate cell adaptation to glutamine starvation and explores their functional division in relation to p53 status. Methods: Using MYC-amplified, p53-mutant (G266E) SF188 glioblastoma cells, we performed siRNA-mediated knockdown, overexpression, and rescue experiments. Cell survival was assessed by trypan blue exclusion and Annexin V/PI staining. ROS levels and NADP⁺/NADPH ratios were measured by DCFH-DA fluorescence and enzymatic assays. Metabolite tracing was conducted using [U-¹³C₅] glutamine followed by LC-MS. Key findings were validated in additional cell lines including HCT116, U2OS and MDA-MB-231. Results: ME1 and ME2 promote SF188 cell survival under glutamine deprivation, an effect that depends on their catalytic activity but is independent of TCA cycle anaplerosis. ME1 maintains redox balance by generating NADPH, and antioxidant treatment rescues the survival defect caused by ME1 knockdown. In contrast, ME2 does not contribute to redox regulation but stabilizes mutant p53 (G266E) via proteasome inhibition. Both of these pro-survival functions are attenuated upon MYC knockdown, suggesting a dependency on MYC expression. Across all cell lines tested, ME1 and ME2 also promote survival through redox maintenance, although the isoform responsible for antioxidant function differs. Conclusions: ME1 and ME2 support metabolic adaptation to glutamine starvation through distinct, isoform-specific mechanisms that depend on MYC expression and p53 mutation status. These findings suggest malic enzymes as potential therapeutic targets in MYC-driven, p53-mutant tumors. Full article

(This article belongs to the Section Cell Metabolism)

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13 pages, 2754 KB

Open AccessArticle

Selected Brain Metabolites and Mitochondrial DNA Copy Number as Potential Markers of Ongoing Neurodegeneration in Patients with Wolfram Syndrome

by Ewa Zmysłowska-Polakowska, Tomasz Płoszaj, Sebastian Skoczylas, Julia Grzybowska-Adamowicz, Dobromiła Barańska, Katarzyna Matera, Aleksandra Palatyńska-Ulatowska, Wojciech Młynarski, Agnieszka Zmysłowska and Michal Ciborowski

Metabolites 2026, 16(4), 281; https://doi.org/10.3390/metabo16040281 - 20 Apr 2026

Abstract

Background: Wolfram syndrome (WFS) is a rare neurodegenerative disease that is genetically determined and inherited in an autosomal recessive manner. Although the first clinical symptom appearing in early childhood is diabetes mellitus, subsequent symptoms are associated with optic nerve atrophy, followed by [...] Read more.

Background: Wolfram syndrome (WFS) is a rare neurodegenerative disease that is genetically determined and inherited in an autosomal recessive manner. Although the first clinical symptom appearing in early childhood is diabetes mellitus, subsequent symptoms are associated with optic nerve atrophy, followed by central nervous system atrophy. Methods: The aim of the study was to analyse magnetic resonance images (MRI) of the brain in combination with single-voxel magnetic resonance spectroscopy (MRS) and to assess the copy number of mitochondrial DNA (mtDNA-CN) in 10 patients with WFS compared with a control group of 17 healthy individuals. Results: A significant decrease in the amount of selected metabolites was observed in WFS patients compared to controls in all assessed brain regions (pons, cerebellum, white matter, thalamus, and hippocampus). For three metabolites, Glutamate (Glu), Glutamate + Glutamine (Glx) and total N-acetylaspartate (TNAA), significant differences in concentrations were found between the study groups in almost all matrices evaluating specific areas of the brain (p < 0.011), with the exception of a trend toward reduced TNAA in the hippocampus (p = 0.065). In addition, patients with WFS had a significant decrease in the mitochondrial-to-nuclear DNA ratio compared to controls (p < 0.0003). Some metabolites, such as N-acetylaspartate and total N-acetylaspartate, showed strong correlations with specific regions of the visual pathway on MRI scans in patients with WFS. Conclusions: Selected brain metabolites and mtDNA-CN may become potential markers of WFS, and the results of this study may be used to define indicators for future therapeutic strategies. Full article

(This article belongs to the Special Issue Brain Metabolic Alterations in Neurodegenerative Diseases)

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19 pages, 714 KB

Open AccessArticle

Red Blood Cell Distribution Width and Neutrophil-to-Lymphocyte Ratio as Markers of Cardiovascular Disease and Vascular Calcification in Chronic Kidney Disease: A Large Cohort Study

by Anastasios Zagaliotis, Athanasios Roumeliotis, Stefanos Roumeliotis, Ioannis E. Neofytou, Garyfallia Varouktsi, Eirini Leptokaridou-Mourtzila, Aikaterini Stamou, Vasiliki Sgouropoulou, Gordana Kocic, Andrej Veljkovic, Rudolf Bittner, Willi Jahnen-Dechent, Leon J. Schurgers and Vassilios Liakopoulos

Metabolites 2026, 16(4), 280; https://doi.org/10.3390/metabo16040280 - 20 Apr 2026

Abstract

Background/Objectives: Cardiovascular disease (CVD) in chronic kidney disease (CKD) arises from a multifaceted interplay of pathophysiological processes, including chronic inflammation, oxidative stress (OS), and accelerated vascular calcification (VC). Red blood cell distribution width (RDW) and the neutrophil-to-lymphocyte ratio (NLR) have emerged as simple, [...] Read more.

Background/Objectives: Cardiovascular disease (CVD) in chronic kidney disease (CKD) arises from a multifaceted interplay of pathophysiological processes, including chronic inflammation, oxidative stress (OS), and accelerated vascular calcification (VC). Red blood cell distribution width (RDW) and the neutrophil-to-lymphocyte ratio (NLR) have emerged as simple, inexpensive, and readily available hematological indices that may capture these underlying disturbances. As such, they hold promise as accessible biomarkers for stratifying cardiovascular risk in patients with CKD. Methods: This cross-sectional study enrolled 497 patients, comprising 477 with CKD across all stages and 20 controls. We evaluated the associations of RDW and NLR with both traditional and non-traditional cardiovascular risk factors, as well as with serum calcification propensity (T50). Spearman’s correlation and multivariable regression analysis were used to assess these relationships. Results: Both RDW and NLR were significantly elevated in patients with established CVD (p < 0.001 for both) and demonstrated a progressive increase across advancing CKD stages (p < 0.001). RDW and NLR showed positive correlations with age, CVD duration, urea, phosphorus, parathormone, CRP, FG23, and mean carotid intima–media thickness (cIMT), while exhibiting inverse correlations with eGFR, serum albumin, hemoglobin, lipids, antioxidants such as superoxide dismutase, fetuin-A, and T50. Additionally, NLR correlated positively with the duration of hypertension and diabetes, as well as with albuminuria. Quartile analysis revealed a stepwise decline in T50 across increasing categories of RDW and NLR, supporting the link with impaired calcification defense. In multivariable analysis, T50 independently predicted NLR (β = −0.013; p = 0.018), whereas total cholesterol (β = −0.011; p = 0.019) and cIMT (β = 0.38; p = 0.018) emerged as independent determinants of RDW. Conclusions: RDW and NLR strongly reflect the burden of inflammation, metabolic disturbance, and vascular dysfunction in patients across the CKD spectrum. The consistent associations with impaired calcification defense and with established cardiovascular risk markers underscore the potential value as accessible indicators of cardiovascular vulnerability in CKD. These findings support incorporating RDW and NLR into routine risk assessment and highlight T50 as a mechanistically relevant determinant of hematologic inflammation profiles. Full article

(This article belongs to the Section Endocrinology and Clinical Metabolic Research)

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16 pages, 15310 KB

Open AccessArticle

Metabolomic Profiling Reveals Geographical Origin, Tissue-Specific Specialization, and Environmental Plasticity in Secondary Metabolism of Dendrobium officinale

by Zhiyong Li, Jian Li, Yue Hu, Xinyi Wu, Xiaojuan Duan, Demin Kong, Xiaowen Li, Jin Cheng and Meina Wang

Metabolites 2026, 16(4), 279; https://doi.org/10.3390/metabo16040279 - 20 Apr 2026

Abstract

Background/Objectives: Dendrobium officinale (D. officinale), an endangered ornamental and medicinal orchid, displays significant variability in its bioactive compounds depending on geographical and environmental factors. To decipher these influences, we investigated metabolic divergence across three cultivars (GN, LS, DX) cultivated in [...] Read more.

Background/Objectives: Dendrobium officinale (D. officinale), an endangered ornamental and medicinal orchid, displays significant variability in its bioactive compounds depending on geographical and environmental factors. To decipher these influences, we investigated metabolic divergence across three cultivars (GN, LS, DX) cultivated in greenhouse and outdoor conditions using untargeted metabolomics. Methods: Metabolites extracted from stem and leaf tissues were analyzed via UHPLC-Q Exactive Orbitrap MS, and the raw data were processed using XCMS for peak alignment and quantification. Differentially abundant metabolites (DAMs) were identified by multivariate statistical analyses including PCA and OPLS-DA. Metabolic pathways were annotated using KEGG, HMDB, and LIPID Maps databases, with enrichment analysis and visualization performed via TBtools II and Hiplot. Results: Metabolite profiling and multivariate analysis revealed distinct chemotypes. The DX cultivar exhibited anthocyanin enrichment in its stems, correlating with a red pigmentation, while GN accumulated specific amino acid derivatives. Tissue-specific metabolic specialization was evident, with leaves displaying greater flavonoid diversity and stems prioritizing lipid and amino acid metabolism. Outdoor cultivation enhanced flavonoid biosynthesis, whereas greenhouse conditions favored alkaloid accumulation. Functional analysis identified both conserved pathways, like phenylpropanoid biosynthesis, and varietal-specific adaptations in amino acid and secondary metabolism. Notably, alkaloid levels declined sharply during plant defoliation. Conclusions: Our findings demonstrate that environmental factors and geographical origin synergistically shape the metabolic profiles of D. officinale. This provides a scientific basis for optimizing cultivation strategies—through targeted environmental adjustments and varietal selection—to enhance the yield of desired bioactive compounds. Full article

(This article belongs to the Special Issue Metabolomics and Plant Defence, 2nd Edition)

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10 pages, 752 KB

Open AccessCommunication

Identification of Primary Hyperoxaluria Type III by Gas Chromatography/Mass Spectrometry-Based Urine Metabolomics

by Tomiko Kuhara, Morimasa Ohse, Tatsuya Fukasawa, Koichi Maruyama and James Pitt

Metabolites 2026, 16(4), 278; https://doi.org/10.3390/metabo16040278 - 19 Apr 2026

Abstract

Objectives: Primary hyperoxaluria type III (PH3) causes kidney stones in children and adults. Gas chromatography/mass spectrometry (GC/MS)-based metabolomics has been applied to study patients with primary hyperoxaluria types I and II, 2,8-dihydroxyadenine lithiasis, and xanthinuria types I to III. This study was performed [...] Read more.

Objectives: Primary hyperoxaluria type III (PH3) causes kidney stones in children and adults. Gas chromatography/mass spectrometry (GC/MS)-based metabolomics has been applied to study patients with primary hyperoxaluria types I and II, 2,8-dihydroxyadenine lithiasis, and xanthinuria types I to III. This study was performed to verify the usefulness of this technique for the diagnosis of PH3. Specifically, we evaluated an 8-month-old infant with recurrent kidney stones. Methods: GC/MS-based metabolomics was performed on spot urine samples using initial urease pretreatment without fractionation. Results: Metabolomics revealed increased levels of 2,4-dihydroxyglutarate and 4-hydroxyglutamate. No simultaneous elevations of these two critical biomarkers were observed in other patients, except for one case of PH3 confirmed by the identification of HOGA1 mutations. A moderate increase in 4-hydroxyglutamate has been observed only in cases of primary hyperammonemia, in which analytes such as orotate, uridine, glutamine, or proline, but not 2,4-dihydroxyglutarate, are biomarkers, thus distinguishing PH3 from primary hyperammonemia. Conclusions: GC/MS-based urine metabolomics enables the rapid screening and chemical diagnosis of PH3 and other congenital anomalies that cause urolithiasis. This technique can also be used to monitor disease progression, as patients with PH3 benefit from long-term follow-up, particularly when transitioning from childhood to adulthood. The timely identification of patients with hereditary urolithiasis is crucial. To address this, a discussion was had about the current diagnostic criteria. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Metabolomics in Disease Biomarker Discovery)

24 pages, 937 KB

Open AccessReview

Diagnostic Criteria and Genetic Basis of Polycystic Ovary Syndrome: A Narrative Review

by María de los Angeles Cepero-González, Adriana Aguilar-Galarza, Víctor Manuel Rodríguez-García, Teresa García-Gasca and Ulisses Moreno Celis

Metabolites 2026, 16(4), 277; https://doi.org/10.3390/metabo16040277 - 19 Apr 2026

Abstract

This study reviews the main candidate genes involved in the pathophysiology of Polycystic Ovary Syndrome (PCOS). PCOS is a common endocrine–metabolic disorder in women of reproductive age, characterized by menstrual irregularity, hyperandrogenism, and polycystic ovarian morphology. It is associated with increased metabolic and [...] Read more.

This study reviews the main candidate genes involved in the pathophysiology of Polycystic Ovary Syndrome (PCOS). PCOS is a common endocrine–metabolic disorder in women of reproductive age, characterized by menstrual irregularity, hyperandrogenism, and polycystic ovarian morphology. It is associated with increased metabolic and cardiovascular risk and is a leading cause of infertility. Although its pathophysiology is not fully understood, alterations in the hypothalamic–pituitary–ovarian axis, insulin metabolism, and steroidogenesis have been described. Polymorphisms in genes encoding hormones, enzymes, and receptors in these pathways contribute to clinical variability and ethnic differences, offering potential for early diagnosis and personalized medicine. This review summarizes key candidate genes related to insulin metabolism (INS, INSR, IRS-1), the hypothalamic–pituitary–ovarian axis (LHβ, LHCGR, FSHR, GnRHR, AMH, AMHR2, KISS1, CAPN10), steroidogenesis (CYP11A, CYP17A1, CYP19A1, CYP21, 17β-HSD, SHBG, AR, STAR), and other clinically relevant mechanisms such as obesity, lipid metabolism (PPARG, VDR, FTO), and follicular development (ACE). Full article

(This article belongs to the Special Issue Endocrine Disruptors, Nutritional Modulators and Metabolic Pathways in PCOS: From Exposure to Intervention)

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18 pages, 13187 KB

Open AccessArticle

Unveiling the Fragrant Secrets of Dendrobium devonianum: Terpenoid Pathways and Floral Scent Dynamics

by Shichao Wang, Shu He, Congjun Yuan, Xingliang Chen, Hoang Van Sam, Wei Chen Lum, Yaquan Dou and Rui Shi

Metabolites 2026, 16(4), 276; https://doi.org/10.3390/metabo16040276 - 18 Apr 2026

Abstract

Background/Objectives: The orchid Dendrobium devonianum Paxt., valued for its ornamental and medicinal properties, is widely used in horticulture, medicine, and food industries. Methods: This study investigated dynamic changes in aroma-active volatile organic compounds (VOCs) and associated gene expression in D. devonianum flowers across [...] Read more.

Background/Objectives: The orchid Dendrobium devonianum Paxt., valued for its ornamental and medicinal properties, is widely used in horticulture, medicine, and food industries. Methods: This study investigated dynamic changes in aroma-active volatile organic compounds (VOCs) and associated gene expression in D. devonianum flowers across four developmental stages (bud, half bloom, full bloom, and aging) using headspace solid-phase microextraction, gas chromatography–mass spectrometry, and transcriptome analysis. Results: Floral VOCs, particularly volatile terpenoids and esters, were most abundant at full bloom. Among the 664 VOCs identified, α-hemelene, β-bisabolene, δ-naphthalene, perillyl alcohol, L-perillyl alcohol, terpinen-4-ol, 2-(4-methylphenyl)propan-2-ol, cis-3-hexenyl butyrate, and α-pinene were likely to contribute to floral scent. Terpene biosynthesis pathways played a pivotal role in floral fragrance formation. A comprehensive terpenoid biosynthesis pathway for D. devonianum floral scent was proposed, and eight genes encoding key regulatory enzymes were identified. Conclusions: These results provide new insights into terpenoid metabolism in Dendrobium and may guide future research on the utilization of floral scent. Full article

(This article belongs to the Section Plant Metabolism)

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20 pages, 5525 KB

Open AccessArticle

Parishin B Attenuates PTZ-Induced Seizures in Zebrafish and Is Associated with Neurotransmitter Balance and ACLY-Related Metabolic Pathways

by Meng Sun, Haida Liu, Zhiying Hou, Qiong Wang and Wu Zhong

Metabolites 2026, 16(4), 275; https://doi.org/10.3390/metabo16040275 - 18 Apr 2026

Abstract

Background: Epilepsy is a chronic neurological disorder characterized by recurrent seizures, complex neurochemical, and metabolic disturbances. Parishin B, a major bioactive component of Gastrodia elata, has shown neuroprotective potential, but its systemic mechanisms remain unclear. Methods: A pentylenetetrazol (PTZ)-induced seizure model in zebrafish [...] Read more.

Background: Epilepsy is a chronic neurological disorder characterized by recurrent seizures, complex neurochemical, and metabolic disturbances. Parishin B, a major bioactive component of Gastrodia elata, has shown neuroprotective potential, but its systemic mechanisms remain unclear. Methods: A pentylenetetrazol (PTZ)-induced seizure model in zebrafish larvae was developed and used to evaluate the anti-seizure effects of Parishin B. Behavioral analysis, ELISA-based biochemical assays, integrated untargeted metabolomics with DIA-based proteomics, and qPCR were performed to decipher underlying molecular mechanisms. Results: Parishin B (0.0625–0.25 mg/mL) significantly alleviated PTZ-induced hyperactivity without developmental toxicity. Parishin B restored neurotransmitter balance by increasing GABA, dopamine, and norepinephrine levels while reducing 5-HT. In addition, it suppressed neuroinflammation and enhanced antioxidant capacity. Integrated multi-omics analysis revealed that Parishin B modulated key metabolic pathways, particularly the TCA cycle and lipid metabolism, and reversed the downregulation of ATP-citrate lyase (ACLY). Parishin B was also associated with the regulation of ferroptosis-related pathways, supported by changes in acsl4a and fth1a expression. qPCR results further confirmed the regulation of aclya, unc13c, and GABAergic signaling genes. Conclusions: Parishin B exerts anti-seizure effects through coordinated regulation of neurotransmitter homeostasis, neuroinflammation, and ACLY-associated energy–lipid metabolism, with potential involvement in ferroptosis-related processes. These findings provide molecular insights supporting Parishin B as a promising candidate for epilepsy therapy. Full article

(This article belongs to the Section Pharmacology and Drug Metabolism)

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16 pages, 5208 KB

Open AccessArticle

Deep Learning-Based and Python-Driven Construction and Application of a Mass Spectrometry Data Analysis Workflow: Taking Glucosinolates as an Example

by Shangshen Yang, Siyu Jia, Peiyu Jia, Wenyu Xie and Xiaoming Wang

Metabolites 2026, 16(4), 274; https://doi.org/10.3390/metabo16040274 - 17 Apr 2026

Abstract

Background: Radish seeds are our model on glucosinolates (GSLs), which is a class of secondary metabolites in medicinal plants of the Brassicaceae family. Multilayer perceptron (MLP) network is highly effective in the study of complex plants. This study came up with a smart [...] Read more.

Background: Radish seeds are our model on glucosinolates (GSLs), which is a class of secondary metabolites in medicinal plants of the Brassicaceae family. Multilayer perceptron (MLP) network is highly effective in the study of complex plants. This study came up with a smart plan through the Python language. Methods: First, we used the MLP network to pick out GSL precursor ions, running them through a deep learning filter. Next, we set up an automated screening system and looked at how standard chemicals break down. To speed things up, we created a scoring system that flagged promising compounds. After that, we built a tracer molecular network, basically connecting compounds according to how the plant makes them, which helped us label everything accurately. Finally, we brought in a math-based tool that pieces together different chemical parts to predict new GSL structures. Results: With this workflow, we annotated 195 glucosinolate-related compounds in radish seeds. That includes 86 regular GSLs, 34 malonyl products, 40 sinapoyl compounds, and 35 diglycosides. Among them, eight compounds were confirmed by comparison with authentic standards (retention time and MS/MS data), whereas the remaining compounds were tentatively annotated based on accurate mass measurements, diagnostic fragment ions, Tracer Molecular Nnetworking, and literature/database matching. In addition, 36 compounds were considered putatively novel derivatives pending further structural confirmation. Conclusions: This new approach reduces the time spent on determining chemicals in complicated samples. This can be done with other vegetables and medicinal herbs by researchers. It assists us in knowing the chemistry of plants in a deeper manner. Full article

(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition)

18 pages, 1356 KB

Open AccessArticle

Bile and Serum Metabolomics in Living Donor Liver Transplantation: Exploratory Insights into Acute Rejection Biomarkers

by Yuta Hirata, Yasunaru Sakuma, Hideo Ogiso, Taiichi Wakiya, Takahiko Omameuda, Toshio Horiuchi, Noriki Okada, Yukihiro Sanada, Yasuharu Onishi, Hironori Yamaguchi, Ryozo Nagai and Kenichi Aizawa

Metabolites 2026, 16(4), 273; https://doi.org/10.3390/metabo16040273 - 17 Apr 2026

Abstract

Background: Acute rejection remains a major complication following liver transplantation, yet reliable noninvasive biomarkers for its early prediction and diagnosis remain unidentified. This exploratory study characterized bile and serum metabolites associated with acute rejection in living donor liver transplantation using comprehensive metabolomic profiling [...] Read more.

Background: Acute rejection remains a major complication following liver transplantation, yet reliable noninvasive biomarkers for its early prediction and diagnosis remain unidentified. This exploratory study characterized bile and serum metabolites associated with acute rejection in living donor liver transplantation using comprehensive metabolomic profiling combined with machine learning. Methods: Non-targeted metabolomics were performed on bile samples collected on post-operative day (POD) 1 (n = 38) and serum on POD 14 (n = 45) from liver transplant recipients. Partial least squares discriminant analysis-based variable selection was followed by logistic regression and least absolute shrinkage and selection operator models, which were evaluated via cross-validation in the discovery cohort to explore potential biomarkers for acute rejection. Results: A three-variable, bile-based model for predicting acute rejection achieved a mean cross-validated AUC of 0.872 (95% confidence interval: 0.814–0.930). Glycohyocholic acid and sulfolithocholylglycine were the main contributors. A nine-variable serum model for the Rejection Activity Index, including the change in γ-glutamyl transferase, showed a mean cross-validated R² of 0.728 (95% confidence interval: 0.609–0.846), with methionine, creatine, and oxidized fatty acids contributing prominently. Conclusions: These findings suggest that metabolomic profiling combined with machine learning may provide candidate biomarkers for acute rejection after liver transplantation. However, given the exploratory nature of the study and the lack of external validation, the clinical utility of these metabolite signatures remains to be determined. Therefore, external validation in larger, independent cohorts will be required. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics in Human Health and Disease)

17 pages, 2939 KB

Open AccessArticle

Untargeted GC-IMS Metabolomics of Wound Headspace for Bacterial Infection Biomarker Discovery

by Yanyi Lu, Bowen Yan, Lin Zeng, Bangfu Zhou, Ruoyu Wu, Xiaozheng Zhong and Qinghua He

Metabolites 2026, 16(4), 272; https://doi.org/10.3390/metabo16040272 - 17 Apr 2026

Abstract

Background/Objectives: Wound infections cause significant morbidity, yet current diagnostics rely on time-consuming microbial culture. Volatile organic compounds (VOCs) from bacterial metabolism offer potential for early diagnosis. This study aimed to validate the volatile metabolites profiled by gas chromatography–ion mobility spectrometry (GC-IMS) combined with [...] Read more.

Background/Objectives: Wound infections cause significant morbidity, yet current diagnostics rely on time-consuming microbial culture. Volatile organic compounds (VOCs) from bacterial metabolism offer potential for early diagnosis. This study aimed to validate the volatile metabolites profiled by gas chromatography–ion mobility spectrometry (GC-IMS) combined with machine learning for rapid identification of wound infections and certain bacterial infections. Methods: Headspace of clinical wound samples were analyzed using GC-IMS. Volatile metabolite profiles were compared between infected and non-infected groups and between Escherichia coli (E. coli)-positive and negative samples. Partial least squares discriminant analysis (PLS-DA) and Mann–Whitney U test were used for preliminary screening with variable importance in projection (VIP) > 1 and p-value < 0.05. Three machine learning algorithms, namely support vector machine (SVM), logistic regression (LR), and random forest (RF), were trained on the selected features for classification, using 5-fold cross-validation with 10 repeated runs. Model performance was assessed using key evaluation metrics, including accuracy, sensitivity, specificity, the area under the curve (AUC) and feature importance ranking to identify the most relevant biomarkers. Results: A total of 19 volatile metabolites associated with clinical wound samples were identified. The RF model achieved 90.15% sensitivity and 0.91 AUC for bacterial infection detection. For E. coli identification, LR reached 85.35% sensitivity and 0.89 AUC. Potential volatile metabolic biomarkers including elevated 3-methyl-1-butanol, 2-methyl-1-butanol, and ethyl hexanoate for identifying bacterial infection were selected through the cross-validation results of the three algorithms. Conclusions: Untargeted metabolomics by GC-IMS effectively captures infection-specific volatile metabolic signatures in complex wound samples. Integration with machine learning enables rapid, high-accuracy diagnosis of bacterial infections and E. coli identification at point of care. This approach addresses clinical metabolomics translational challenges by providing a portable and cost-effective method, potentially reducing antibiotic misuse through more timely and targeted therapy. Full article

(This article belongs to the Special Issue New Findings on Microbial Metabolism and Its Effects on Human Health)

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23 pages, 3083 KB

Open AccessArticle

Dynamic Role of Omega-3/Omega-6 Polyunsaturated Fatty Acid Ratio in Modulation of Adipogenicity, Lipid Metabolites, and Adipokines Associated with Platelet Hyperactivity

by Sultanah Turki Almolafikh, Pandurangan Subash-Babu, Tlili Barhoumi and Ali A Alshatwi

Metabolites 2026, 16(4), 271; https://doi.org/10.3390/metabo16040271 - 17 Apr 2026

Abstract

Background: Unhealthy expansion of adipose tissue (AT) due to excessive dietary intake of omega-6 or overnutrition stimulates the overaccumulation of the extracellular matrix (ECM), resulting in AT metabolic dysregulation. Hypertrophic conditions, excessive adipose depots, and hypoxia stimulate the overproduction of collagenous and non-collagenous [...] Read more.

Background: Unhealthy expansion of adipose tissue (AT) due to excessive dietary intake of omega-6 or overnutrition stimulates the overaccumulation of the extracellular matrix (ECM), resulting in AT metabolic dysregulation. Hypertrophic conditions, excessive adipose depots, and hypoxia stimulate the overproduction of collagenous and non-collagenous proteins, which pathophysiologically initiate the pro-fibrotic signaling pathway associated with fibrosis progression, resulting in atherosclerosis and cardiovascular diseases. Methods: We aimed to investigate adipocyte plasticity in response to a varying ratio of omega-3 (ω3) to omega-6 (ω6) supplementation during the chemically induced adipogenic differentiation of human mesenchymal stem cells. Additionally, changes in lipid accumulation, adipocyte hypertrophy and hyperplasia, active lipid metabolites, and inflammatory cytokine profiles were evaluated. Furthermore, conditioned media from adipocytes treated with different ω3/ω6 ratios were applied to platelets to assess inflammatory responses through prostaglandin and thromboxane measurements. Results: A 1:3 ratio of ω3/ω6 (20:60 µM) significantly reduced lipid accumulation, promoted brown-like adipocyte morphology, and decreased apoptosis and reactive oxygen species (ROS) generation, as confirmed via FACS analysis. Transcriptional control of adipose tissue expansion was confirmed by the downregulation of LIPIN1 and COL1A1 mRNA expression and p-prostaglandin12-R protein levels in a 1:3 ratio when compared with 1:1, 1:2, 1:4, or 2:6 ratios of ω3/ω6. Notably, a 1:3 ratio of fatty-acid-treated adipocyte-conditioned media-treated platelets significantly reduced platelet activation and aggregation, as evidenced by lower p-thromboxane A2 protein levels. Conclusions: Supplementation with a 1:3 (20:60 µM) ω3/ω6 ratio favored the development of lean adipocytes, evidenced by the decreased lipid storage achieved by mitochondrial thermogenesis, which attenuated minimal adipocyte expansion and metabolic inflammation. Full article

(This article belongs to the Section Advances in Metabolomics)

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12 pages, 231 KB

Open AccessArticle

Association Between Vitamin D Deficiency and Glycemic, Lipid, and Adiposity Markers in Older Adults: A Nationally Representative Study

by Yong-Joon Kim and Kyeongmin Jang

Metabolites 2026, 16(4), 270; https://doi.org/10.3390/metabo16040270 - 16 Apr 2026

Abstract

Background/Objectives: Vitamin D plays an important role in glucose metabolism, lipid regulation, and inflammatory processes, and has been implicated in cardiometabolic health. However, its associations with specific metabolic biomarkers remain inconsistent, particularly in older adults. This study aimed to examine whether vitamin D [...] Read more.

Background/Objectives: Vitamin D plays an important role in glucose metabolism, lipid regulation, and inflammatory processes, and has been implicated in cardiometabolic health. However, its associations with specific metabolic biomarkers remain inconsistent, particularly in older adults. This study aimed to examine whether vitamin D deficiency is differentially associated with multiple metabolic biomarkers in a nationally representative sample of older adults. Methods: This cross-sectional study used data from the 2024 Korea National Health and Nutrition Examination Survey, including 1806 adults aged ≥65 years. Vitamin D deficiency was defined as serum 25-hydroxyvitamin D levels < 20 ng/mL. Metabolic biomarkers included fasting glucose, glycated hemoglobin (HbA1c), triglycerides, C-reactive protein (CRP), high-density lipoprotein cholesterol (HDL-C), waist circumference, and body mass index (BMI). Complex sample linear regression analyses were performed with sequential adjustment for sociodemographic factors, health behaviors, and comorbidities. Results: In unadjusted analyses, vitamin D deficiency was associated with adverse metabolic profiles, including higher fasting glucose, HbA1c, triglycerides, waist circumference, and CRP levels, and lower HDL-C levels. After adjustment for sociodemographic factors, health behaviors, and comorbidities, significant associations remained for HbA1c (β = 0.10, p = 0.034), triglycerides (β = 0.10, p = 0.003), and waist circumference (β = 1.21, p = 0.040). No significant associations were observed for fasting glucose, HDL-C, CRP, or BMI. Conclusions: Vitamin D deficiency was independently associated with poorer long-term glycemic status, hypertriglyceridemia, and central adiposity in older adults, but not with other metabolic markers after adjustment. These findings suggest that the metabolic correlates of vitamin D deficiency may be domain-specific rather than generalized. Longitudinal and interventional studies are needed to clarify causality and underlying mechanisms. Full article

(This article belongs to the Section Endocrinology and Clinical Metabolic Research)

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