Metabolomics Technology Research Articles

The molecular and metabolic events behind different germination stages of rice seeds: A metabolomics perspective

AbstractSeed germination is a crucial stage for the completion of plants' life cycle. The process of seed germination is a very important phenomenon for agricultural food and crop production and to understand the underlying food chemistry. Rice (Oryza sativa L.) being easy to grow and cheap source of phytonutrients is a fundamental food crop across the world. Several researches are going on for years to improve the production of rice, ameliorate the deadly bacterial or fungal diseases utilizing genetics, transcriptomics, and proteomics aspects. Metabolomics is a very new arena of research in this field. With the help of modern‐day metabolomic tools and technologies, researchers are incessantly trying to unveil the metabolic construction of rice seeds, and new to this topic is seed germination. The principal aim of this review on metabolomics of germinating rice seeds is to have a big picture on the key molecular, cellular, and metabolic events of germination. This review tries to summarize all the available data to fulfill the aforesaid aim.

The colibactin-producing Escherichia coli alters the tumor microenvironment to immunosuppressive lipid overload facilitating colorectal cancer progression and chemoresistance

ABSTRACT Intratumoral bacteria flexibly contribute to cellular and molecular tumor heterogeneity for supporting cancer recurrence through poorly understood mechanisms. Using spatial metabolomic profiling technologies and 16SrRNA sequencing, we herein report that right-sided colorectal tumors are predominantly populated with Colibactin-producing Escherichia coli (CoPEC) that are locally establishing a high-glycerophospholipid microenvironment with lowered immunogenicity. It coincided with a reduced infiltration of CD8+ T lymphocytes that produce the cytotoxic cytokines IFN-γ where invading bacteria have been geolocated. Mechanistically, the accumulation of lipid droplets in infected cancer cells relied on the production of colibactin as a measure to limit genotoxic stress to some extent. Such heightened phosphatidylcholine remodeling by the enzyme of the Land’s cycle supplied CoPEC-infected cancer cells with sufficient energy for sustaining cell survival in response to chemotherapies. This accords with the lowered overall survival of colorectal patients at stage III-IV who were colonized by CoPEC when compared to patients at stage I-II. Accordingly, the sensitivity of CoPEC-infected cancer cells to chemotherapies was restored upon treatment with an acyl-CoA synthetase inhibitor. By contrast, such metabolic dysregulation leading to chemoresistance was not observed in human colon cancer cells that were infected with the mutant strain that did not produce colibactin (11G5∆ClbQ). This work revealed that CoPEC locally supports an energy trade-off lipid overload within tumors for lowering tumor immunogenicity. This may pave the way for improving chemoresistance and subsequently outcome of CRC patients who are colonized by CoPEC.

Intrauterine Growth Restriction Affects Colonic Barrier Function via Regulating the Nrf2/Keap1 and TLR4-NF-κB/ERK Pathways and Altering Colonic Microbiome and Metabolome Homeostasis in Growing-Finishing Pigs.

Intrauterine growth restriction (IUGR) pigs are characterized by long-term growth failure, metabolic disorders, and intestinal microbiota imbalance. The characteristics of the negative effects of IUGR at different growth stages of pigs are still unclear. Therefore, this study explored through multi-omics analyses whether the IUGR damages the intestinal barrier function and alters the colonization and metabolic profiles of the colonic microbiota in growing-finishing pigs. Seventy-two piglets (36 IUGR and 36 NBW) were allocated for this trial to analyze physiological and plasma biochemical parameters, as well as oxidative damage and inflammatory response in the colon. Moreover, the colonic microbiota communities and metabolome were examined using 16s rRNA sequencing and metabolomics technologies to reveal the intestinal characteristics of IUGR pigs at different growth stages (25, 50, and 100 kg). IUGR altered the concentrations of plasma glucose, total protein, triglycerides, and cholesterol. Colonic tight junction proteins were markedly inhibited by IUGR. IUGR decreased plasma T-AOC, SOD, and GSH levels and colonic SOD-1, SOD-2, and GPX-4 expressions by restraining the Nrf2/Keap1 signaling pathway. Moreover, IUGR increased colonic IL-1β and TNF-α levels while reducing IL-10, possibly through activating the TLR4-NF-κB/ERK pathway. Notably, IUGR pigs had lower colonic Streptococcus abundance and Firmicutes-to-Bacteroidetes ratio at the 25 kg BW stage while having higher Firmicutes abundance at the 100 kg BW stage; moreover, IUGR pigs had lower SCFA concentrations. Metabolomics analysis showed that IUGR increased colonic lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds concentrations and enriched three differential metabolic pathways, including linoleic acid, sphingolipid, and purine metabolisms throughout the trial. Collectively, IUGR altered the nutrient metabolism, redox status, and colonic microbiota community and metabolite profiles of pigs and continued to disrupt colonic barrier function by reducing antioxidant capacity via the Nrf2/Keap1 pathway and activating inflammation via the TLR4-NF-κB/ERK pathway during the growing-finishing stage. Moreover, colonic Firmicutes and Streptococcus could be potential regulatory targets for modulating the metabolism and health of IUGR pigs.

Dietary Chinese herbal formula supplementation improves yolk fatty acid profile in aged laying hens

Chinese herbal formula (CHF) has the potential to improve the performance of aged laying hens through integrated regulation of various physiological functions. The present study aimed to investigate the effects of dietary CHF supplementation on the yolk fatty acid profile in aged laying hens. A total of 144 healthy 307-day-old Xinyang black-feather laying hens were randomly allocated into two groups: a control group (CON, fed a basal diet) and a CHF group (fed a basal diet supplemented with 1% CHF; contained 0.30% Leonurus japonicus Houtt., 0.20% Salvia miltiorrhiza Bge., 0.25% Ligustrum lucidum Ait., and 0.25% Taraxacum mongolicum Hand.-Mazz. for 120 days). The fatty acid concentrations in egg yolks were analyzed using a targeted metabolomics technology at days 60 and 120 of the trial. The results showed that dietary CHF supplementation increased (p < .05) the concentrations of several saturated fatty acids (SFA, including myristic acid and stearic acid), monounsaturated fatty acids (MUFA, including petroselinic acid, elaidic acid, trans-11-eicosenoic acid, and cis-11-eicosenoic acid), polyunsaturated fatty acids (PUFA, including linolelaidic acid, linoleic acid, γ-linolenic acid, α-linolenic acid, 11c,14c-eicosadienoic acid, eicosatrienoic acid, homo-γ-linolenic acid, arachidonic acid, and docosapentaenoic acid), and fatty acid indexes (total MUFA, n-3 and n-6 PUFA, PUFA/SFA, hypocholesterolemic/hypercholesterolaemic ratio, health promotion index, and desirable fatty acids) in egg yolks. Collectively, these findings suggest that dietary CHF supplementation could improve the nutritional value of fatty acids in egg yolks of aged laying hens, which would be beneficial for the production of healthier eggs to meet consumer demands.

Application of metabolomics in oral squamous cell carcinoma.

Oral squamous cell carcinoma (OSCC) is a prevalent malignancy affecting the head and neck region. The prognosis for OSCC patients remains unfavorable due to the absence of precise and efficient early diagnostic techniques. Metabolomics offers a promising approach for identifying distinct metabolites, thereby facilitating early detection and treatment of OSCC. This review aims to provide a comprehensive overview of recent advancements in metabolic marker identification for early OSCC diagnosis. Additionally, the clinical significance and potential applications of metabolic markers for the management of OSCC are discussed. This review summarizes metabolic changes during the occurrence and development of oral squamous cell carcinoma and reviews prospects for the clinical application of characteristic, differential metabolites in saliva, serum, and OSCC tissue. In this review, the application of metabolomic technology in OSCC research was summarized, and future research directions were proposed. Metabolomics, detection technology that is the closest to phenotype, can efficiently identify differential metabolites. Combined with statistical data analyses and artificial intelligence technology, it can rapidly screen characteristic biomarkers for early diagnosis, treatment, and prognosis evaluations.

Pharmacodynamics and mechanism of Erigeron breviscapus granules in the treatment of ischemic stroke in mice by regulating sphingolipid metabolism based on metabolomics

AimErigeron breviscapus (Vant.) Hand.-Mazz. (EB) granules is the extract preparation of EB, with clear curative effect and unclear mechanism. This study intends to systematically explore the specific mechanism of EB granules in the treatment of IS from the metabolic perspective. MethodsThe model of transient middle cerebral artery occlusion (tMCAO) in mice was established by the suture-occluded method. The therapeutic effect of EB granules on tMCAO mice was evaluated by behavioral evaluation, brain water content determination, 2,3,5-triphenyltetrazolium chloride (TTC) staining, hematoxylin-eosin (HE) staining, and levels of lactate dehydrogenase (LDH) and neuron specific enolase (NSE) in serum. In order to screen differential metabolites, non-targeted metabolomics technology was used to detect the metabolites in serum before and after administration. Univariate statistics, multivariate statistics and bioinformatics were used to analyze the changes of metabolites in serum of tMCAO mice. The possible related mechanism of EB granules in treating IS was screened by pathway enrichment analysis, and the preliminary verification was carried out at animal level by enzyme linked immunosorbent assay (ELISA) and western blot (WB). ResultsEB granules could significantly improve behavior of tMCAO mice, reduce brain water content and cerebral infarction volume, improve morphology of brain tissue, reduce the levels of LDH and NSE in serum. A total of 232 differential metabolites were screened, which were mainly enriched in many biological processes such as sphingolipid metabolism. The differential metabolite S1P and its receptors S1PR1 and S1PR2 in sphingolipid metabolism were verified. The results showed that the level of S1P in brain tissue increased and the protein expression of S1PR1 decreased significantly after modeling, and reversed after administration, but there was no significant difference in the protein expression of S1PR2. ConclusionThe therapeutic effects of EB granules may be related to affecting sphingolipid metabolism through regulating S1P/S1PR1.

Metabolome profiling by widely-targeted metabolomics and biomarker panel selection using machine-learning for patients in different stages of chronic kidney disease

Chronic kidney disease (CKD) is an increasingly prevalent medical condition associated with high mortality and cardiovascular complications. The intricate interplay between kidney dysfunction and subsequent metabolic disturbances may provide insights into the underlying mechanisms driving CKD onset and progression. Herein, we proposed a large-scale plasma metabolite identification and quantification system that combines the strengths of targeted and untargeted metabolomics technologies, i.e., widely-targeted metabolomics (WT-Met) approach. WT-Met method enables large-scale identification and accurate quantification of thousands of metabolites. We collected plasma samples from 21 healthy controls and 62 CKD patients, categorized into different stages (22 in stages 1–3, 20 in stage 4, and 20 in stage 5). Using LC-MS-based WT-Met approach, we were able to effectively annotate and quantify a total of 1431 metabolites from the plasma samples. Focusing on the 539 endogenous metabolites, we identified 399 significantly altered metabolites and depicted their changing patterns from healthy controls to end-stage CKD. Furthermore, we employed machine-learning to identify the optimal combination of metabolites for predicting different stages of CKD. We generated a multiclass classifier consisting of 7 metabolites by machine-learning, which exhibited an average AUC of 0.99 for the test set. In general, amino acids, nucleotides, organic acids, and their metabolites emerged as the most significantly altered metabolites. However, their patterns of change varied across different stages of CKD. The 7-metabolite panel demonstrates promising potential as biomarker candidates for CKD. Further exploration of these metabolites can provide valuable insights into their roles in the etiology and progression of CKD.

Integrated analysis of metabolomic and gut microbiota reveals idiosyncratic drug-induced liver injury resulting from the combined administration of bavachin and icariside II

Objective: Xianling gubao (XLGB), a widely used Chinese patent medicine for osteoporosis, has garnered significant attention due to its potential to cause liver injury. The constituents Psoraleae Fructus (PF, the dried ripe seeds of Psoralea corylifolia L.) and Epimedii Folium (EF, the dried leaves of various Epimedium species) present in XLGB have been implicated in causing idiosyncratic drug-induced liver injury (IDILI). However, the specific components and mechanisms underlying liver injury related to these tonics remain elusive. This study aims to establish that the combination of bavachin (the primary active compound in PF, and icariside II, the main active compound in EF) induces IDILI in a tumor necrosis factor-α (TNF-α)-mediated mouse model. Methods: To assess the impact of bavachin and icariside II on the liver in the presence of TNF-α immune stress, an animal model was developed. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics technology was employed to identify biomarkers associated with TNF-α-induced IDILI and the combination of bavachin and icariside II. Additionally, 16S rRNA high-throughput sequencing technology was utilized to explore changes in the species composition and relative abundance of gut microbiota. Spearman correlation analysis was conducted to unveil the relationship between gut microbiota and in vivo metabolites. Results: The study observed that the combined administration of bavachin and icariside II induced liver injury in the TNF-α mediated susceptibility mouse model of IDILI. Under TNF-α stimulation, there was an elevation in levels in mouse livers following bavachin and icariside II administration, while Gly-Tyr, Leu-Gly, and Trp-Ser levels decreased. These differentially expressed metabolites associated with liver injury were predominantly enriched in metabolic pathways such as sphingolipid metabolism, sphingolipid signaling pathway, and necroptosis. it is noteworthy that the gut of mice with liver injury induced by the bavachin and icariside II combination exhibited a significant increase in Bacteroides and Desulfovibrionaceae abundance. Correlation analysis revealed a positive association between Bacteroidaceae and Desulfovibrionaceae with methylcarbamoyl PAF and methyl Indole-3-acetate, while a negative correlation was observed with Gly-Tyr, Leu-Gly, and Trp-Ser. Conclusions: These findings demonstrated that the combination of bavachin and icariside II increased the risk of IDILI in vivo, providing a promising scientific basis for understanding the component basis of IDILI resulting from the compatibility of EF and PF.

Research progress of metabolomics in children with irritable bowel syndrome

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by symptoms such as abdominal pain, diarrhea, constipation, and indigestion. Given its unclear etiology and pathogenesis, and the absence of specific biomarkers, clinical diagnosis and treatment of IBS continue to pose significant challenges. In recent years, metabolomics technology, known for its non-invasive, high-throughput, high-precision, and highly reproducible features, has been widely applied in the diagnosis, treatment, and prognosis of various diseases. Therefore, metabolomics technology is expected to offer novel insights and methodologies for the biological mechanism research, diagnosis, and treatment of IBS. This article reviews recent advancements in the application of metabolomics to IBS, exploring its potential value in the clinical diagnosis and treatment of children with this condition.

Metabolomic interference induced by short-chain chlorinated paraffins in human normal hepatic cells

Short-chain chlorinated paraffins (SCCPs) are an emerging class of persistent organic pollutants (POPs) that are widely detected in environmental matrices and human samples. Because of their environmental persistence, long-range transport potential, bioaccumulation potential, and biotoxicity, SCCPs pose a significant threat to human health. In this study, metabolomics technology was applied to reveal the metabolomic interference in human normal hepatic (L02) cells after exposure to low (1 μg/L), moderate (10 μg/L), and high (100 μg/L) doses of SCCPs. Principal component analysis (PCA) and metabolic effect level index (MELI) values showed that all three SCCP doses caused notable metabolic perturbations in L02 cells. A total of 72 metabolites that were annotated by MS/MS and matched with the experimental spectra in the Human Metabolome Database (HMDB) or validated by commercially available standards were selected as differential metabolites (DMs) across all groups. The low-dose exposure group shared 33 and 36 DMs with the moderate- and high-dose exposure groups, respectively. The moderate-dose exposure group shared 46 DMs with the high-dose exposure group. In addition, 33 DMs were shared among the three exposure groups. Among the 72 DMs, 9, 9, and 45 metabolites participated in the amino acid, nucleotide, and lipid metabolism pathways, respectively. The results of pathway enrichment analysis showed that the most relevant metabolic pathways affected by SCCPs were the lipid metabolism, fatty acid β-oxidation, and nucleotide metabolism pathways, and that compared with low-dose exposure, moderate- and high-dose SCCP exposures caused more notable perturbations of these metabolic pathways in L02 cells. Exposure to SCCPs perturbed glycerophospholipid and sphingolipid metabolism. Significant alterations in the levels of phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins indicated SCCP-induced biomembrane damage. SCCPs inhibited fatty acid β-oxidation by decreasing the levels of short- and medium-chain acylcarnitines in L02 cells, indicating that the energy supplied by fatty acid oxidation was reduced in these cells. Furthermore, compared with low- and moderate-dose SCCPs, high-dose SCCPs produced a significantly stronger inhibition of fatty acid β-oxidation. In addition, SCCPs perturbed nucleotide metabolism. The higher hypoxanthine levels observed in L02 cells after SCCP exposures indicate that SCCPs may induce several adverse effects, including hypoxia, reactive oxygen species production, and mutagenesis in L02 cells.

Serum metabonomic study to explore the amelioration mechanisms of co‐fermented collagen peptide‐jackfruit juice on the immunosuppressed mice

AbstractThe main purpose of this study was to investigate the improvement effect and serum metabolomic analysis of co‐fermented collagen peptide‐jackfruit juice (FPJ) against immunosuppression in cyclophosphamide‐induced mice. Serum samples were analyzed using ultra‐performance liquid chromatography coupled with mass spectrometry (UPLC‐MS/MS) targeted metabolomics technology, including the normal group, model group, and FPJ group, and determine if such treatments were able to revert immunosuppression‐related metabolic changes to normal status. The results showed that 32 differential metabolites were upregulated and 42 metabolites were downregulated in the model group compared with the normal group. After FPJ intervention, there was a trend of normal callback. Adenosine, inosine, guanosine, 2‐deoxyadenosine, hypoxanthine, xanthine, d‐xylulose‐5‐phosphate, ribulose‐5‐phosphate, phenylpyruvic acid, hippuric acid, 3‐(3‐hydroxyphenyl)‐propionic acid, 3‐ureidopropionate, uridine, dCDP and malonic acid may be used as predictive markers of immunosuppression. Notably, these biomarkers were involved in purine metabolism, pentose phosphate pathway, phenylalanine metabolism, and pyrimidine metabolism. In this study, FPJ inhibited oxidative stress and improved the gut microbes by regulating the disorders of metabolic pathways. The metabolomics approach developed herein provides novel insight into the metabolic disturbances associated with immunosuppression, which will contribute to understanding the mechanism of FPJ on immunosuppression further and providing a basis for further research.

Exploring metabolic responses and pathway changes in CHO-K1 cells under varied aeration conditions and copper supplementations using 1 H NMR-based metabolomics.

The optimization of bioprocess for CHO cell culture involves careful consideration of factors such as nutrient consumption, metabolic byproduct accumulation, cell growth, and monoclonal antibody (mAb) production. Valuable insights can be obtained by understanding cellular physiology to ensure robust and efficient bioprocess. This study aims to improve our understanding of the CHO-K1 cell metabolism using 1 H NMR-based metabolomics. Initially, the variations in culture performance and metabolic profiles under varied aeration conditions and copper supplementations were thoroughly examined. Furthermore, a comprehensive metabolic pathway analysis was performed to assess the impact of these conditions on the implicated pathways. The results revealed substantial alterations in the pyruvate metabolism, histidine metabolism, as well as phenylalanine, tyrosine and tryptophan biosynthesis, which were especially evident in cultures subjected to copper deficiency conditions. Conclusively, significant metabolites governing cell growth and mAb titer were identified through orthogonal partial least square-discriminant analysis (OPLS-DA). Metabolites, including glycerol, alanine, formate, glutamate, phenylalanine, and valine, exhibited strong associations with distinct cell growth phases. Additionally, glycerol, acetate, lactate, formate, glycine, histidine, and aspartate emerged as metabolites influencing cell productivity. This study demonstrates the potential of employing 1 H NMR-based metabolomics technology in bioprocess research. It provides valuable guidance for feed medium development, feeding strategy design, bioprocess parameter adjustments, and ultimately the enhancement of cell proliferation and mAb yield.

Metabolomic and Growth Responses of Houttyunia cordata to Varying Light Intensities and Subsequent Effects on Fermented Products

Suitable light intensities were studied to enable sustainable and efficient cultivation of Houttuynia cordata with a high yield of bioactive compounds which later can be a good quality material for fermentation. To achieve this goal, the evaluation of physiological adaptation and elucidation of the metabolic alterations of Houttuynia cordata in response to different light intensities were conducted. Four-month-old H. cordata was exposed to 3 different light intensities: high light, control, and low light (100, 50 and 20 % natural irradiances, respectively). Physiological responses were measured using leaf gas exchange. The same leaf samples were either methanolic extracted for LC-QTOF-MS analysis to generate metabolite fingerprints or fermented for 3 months prior to quercetin quantification. High light treatment had the greatest effects on both the physiology and metabolisms of H. cordata compared to control and low light treatments. Compared to the control, the key results observed in high-light-grown H. cordata were a significant increase in photosynthesis, a decrease in relative chlorophyll contents, the enrichment of the top 3 metabolic pathways (phenylpropanoid biosynthesis, pyruvate metabolism and fatty acid degradation) and increasing quercetin concentrations in both fresh and fermented leaves. Metabolite fingerprints of high light-grown H. cordata were distinctively different from those of the other 2 treatments according to PCA and hierarchical clustering analysis. In conclusion, H. cordata responded to high light intensity by enriching the phenylpropanoid biosynthetic pathway to elevate sunscreen pigments. Additional acetyl-CoA generated from pyruvate metabolism and fatty acid degradation was a key supporting factor in the above response. As high quercetin concentration was observed in both fresh and fermented leaves, this will lead to quality improvement of the fermented products. HIGHLIGHTS The remarkable effects of light intensities on Houttuynia cordata growth and abundance of bioactive compounds are substantial, but the underlying mechanism has never been investigated. Metabolomics technology was applied to gain insight into light-induced metabolic reconfiguration. GRAPHICAL ABSTRACT

Analysis of contents of different kinds of fatty acids in carotid atherosclerotic plaques

Objective: To analyze the contents of different kinds of fatty acids in carotid atherosclerotic plaques. Methods: A total of 24 patients who underwent carotid endarterectomy at the Second Affiliated Hospital of Naval Medical University from October 2021 to September 2022 due to moderate and severe carotid artery stenosis were retrospectively enrolled, including 20 males and 4 females, with a median age[M(Q1, Q3)] of 68.5 (63.5, 72.3) years. According to the symptoms of cerebral ischemia, the patients were divided into a symptomatic group (12 cases) and an asymptomatic group (12 cases). Regarding the pathological characteristics, the patients were divided into a stable group (14 cases) and a vulnerable group (10 cases) according to carotid plaque pathology scores. The expression differences of different types of fatty acids in carotid plaques were analyzed by targeted fatty acid metabolomics technology based on ultra-performance liquid chromatography-mass spectrometry (UPLC-ESI-MS/MS) analysis. Results: In the 24 samples, the median amount of fatty acids [M (Q1, Q3)] was 1 113 (330, 5 897) ng/g. A total of 13 medium and long-chain fatty acids were detected, including saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids. The content of saturated fatty acids was 584 (290, 9 888) ng/g, accounting for the highest proportion of 51.8%. The content of polyunsaturated fatty acids was 1 444 (393, 4 264) ng/g, accounting for 44.4%. The content of monounsaturated fatty acids was 2 793 (1 558, 3 247) ng/g, accounting for 3.8%. The contents of linoleic acid, α-linolenic acid and oleic acid in carotid plaques in the symptomatic group were 1 760 (581, 3 006), 682 (527, 886) and 2 081 (1 358, 2 907) ng/g, respectively, which were lower than those in the asymptomatic group 3 149 (2 226, 4 683), 1 423 (964, 2 270) and 3 178 (2 352, 3 993) ng/g (all P<0.05). The contents of linoleic acid, α-linolenic acid and oleic acid in carotid plaques in the vulnerable group were 1 537 (588, 2 921), 649 (477, 850) and 2 081 (1 129, 2 831) ng/g, respectively, which were lower than those in the stable group 3 149 (2 047, 4 416), 1 423 (940, 2 184) and 3 091 (2 201, 3 973) ng/g (all P<0.05). There were no significant differences in the contents of 11, 14-eicosadienoic acid, γ-linolenic acid, eicosapentaenoic acid, arachidonic acid, erucic acid, margaric acid, pentadecanoic acid, stearic acid, dodecanoic acid and palmitic acid (all P>0.05). Conclusions: Saturated fatty acids are the main type in carotid plaques. The contents of oleic acid, α-linolenic acid and linoleic acid decrease in vulnerable plaques.

Combined Transcriptomics and Metabolomics Identify Regulatory Mechanisms of Porcine Vertebral Chondrocyte Development In Vitro.

Porcine body length is closely related to meat production, growth, and reproductive performance, thus playing a key role in the profitability of the pork industry. Cartilage development is critical to longitudinal elongation of individual vertebrae. This study isolated primary porcine vertebral chondrocytes (PVCs) to clarify the complex mechanisms of elongation. We used transcriptome and target energy metabolome technologies to confirm crucial genes and metabolites in primary PVCs at different differentiation stages (0, 4, 8, and 12 days). Pairwise comparisons of the four stages identified 4566 differentially expressed genes (DEGs). Time-series gene cluster and functional analyses of these DEGs revealed four clusters related to metabolic processes, cartilage development, vascular development, and cell cycle regulation. We constructed a transcriptional regulatory network determining chondrocyte maturation. The network indicated that significantly enriched transcription factor (TF) families, including zf-C2H2, homeobox, TF_bZIP, and RHD, are important in cell cycle and differentiation processes. Further, dynamic network biomarker (DNB) analysis revealed that day 4 was the tipping point for chondrocyte development, consistent with morphological and metabolic changes. We found 24 DNB DEGs, including the TFs NFATC2 and SP7. Targeted energy metabolome analysis showed that most metabolites were elevated throughout chondrocyte development; notably, 16 differentially regulated metabolites (DRMs) were increased at three time points after cell differentiation. In conclusion, integrated metabolome and transcriptome analyses highlighted the importance of amino acid biosynthesis in chondrocyte development, with coordinated regulation of DEGs and DRMs promoting PVC differentiation via glucose oxidation. These findings reveal the regulatory mechanisms underlying PVC development and provide an important theoretical reference for improving pork production.

Research advances in the application of metabolomics in exercise science.

Exercise training can lead to changes in the metabolic composition of an athlete's blood, the magnitude of which depends largely on the intensity and duration of exercise. A variety of behavioral, biochemical, hormonal, and immunological biomarkers are commonly used to assess an athlete's physical condition during exercise training. However, traditional invasive muscle biopsy testing methods are unable to comprehensively detect physiological differences and metabolic changes in the body. Metabolomics technology is a high-throughput, highly sensitive technique that provides a comprehensive assessment of changes in small molecule metabolites (molecular weight <1,500Da) in the body. By measuring the overall metabolic characteristics of biological samples, we can study the changes of endogenous metabolites in an organism or cell at a certain moment in time, and investigate the interconnection and dynamic patterns between metabolites and physiological changes, thus further understanding the interactions between genes and the environment, and providing possibilities for biomarker discovery, precise training and nutritional programming of athletes. This paper summaries the progress of research on the application of exercise metabolomics in sports science, and looks forward to the future development of exercise metabolomics, with a view to providing new approaches and perspectives for improving human performance, promoting exercise against chronic diseases, and advancing sports science research.

Gut microbiota and metabolites exhibit different profiles after very-low-caloric restriction in patients with type 2 diabetes.

To investigate the effect of short-term very-low-calorie restriction (VLCR) on metabolism in patients with type 2 diabetes (T2D), and elucidate the molecular mechanism through analyses on gut microbiota and small-molecule metabolites. Fourteen T2D patients were hospitalized to receive VLCR (300-600 kcal/d) for 9 days. BMI, BP, and HR were taken before and after VLCR. Levels of blood lipids, fasting insulin, FBG, and 2h PBG were assessed. The microbial diversity in feces was detected by 16S rDNA high-throughput sequencing technology, and small-molecule metabolites in plasma and feces by untargeted metabolomics technology. After VLCR, BW, BMI, WC, BP, and levels of FBG and 2h PBG, insulin, HOMA-IR, and triglyceride decreased significantly in T2D patients (P<0.05). There was no significant change in the α-diversity of fecal microbiota, but the abundance of Bacteroidetes increased significantly, and the Firmicutes/Bacteroidetes ratio decreased significantly from 11.79 to 4.20. Parabacteroides distasonis showed an abundance having increased most prominently after VLCR treatment. Plasma level of amino acid metabolite L-arginine increased significantly. Plasma levels of three lipid metabolites, PC (14:0/20:4 [8Z, 11Z, 14Z, 17Z]), LysoPC (16:1 [9Z]) and LysoPC (18:1 [11Z]), were significantly reduced. Fecal levels of lipid metabolite LysoPC (18:1 [11Z]) and bile acid metabolite glycholic acid were significantly decreased. In T2DM patients, VLCR can considerably reduce body weight and improve glucose and lipid metabolism without causing severe side effects. LysoPC (18:1 [11Z]) and Parabacteroides distasonis showed the most obvious difference after VLCR, which could be the indicators for VLCR in T2D.

The Untargeted Metabolomics Reveals Differences in Energy Metabolism in Patients with Different Subtypes of Ischemic Stroke.

Ischemic stroke (IS) is the most common subtype of stroke. The risk factors and pathogenesis of IS are complex and varied due to different subtypes. Therefore, we used metabolomics technology to investigate the biomarkers and potential pathophysiological mechanisms of different subtypes of IS. We included 126 IS patients and divided them into two groups based on the TOAST classification: large-artery atherosclerosis (LAA) group (n = 87) and small-vessel occlusion (SVO) group (n = 39). Plasma metabolomics analysis was performed using liquid chromatography-high-resolution mass spectrometry (LC-HRMS) to identify metabolic profiles in LAA and SVO subtype IS patients and to determine metabolic differences between patients with the two subtypes of IS. We identified 26 differential metabolites between LAA and SVO subtype IS. A multiple prediction model based on the plasm metabolites had good predictive ability for IS subtyping (AUC = 0.822, accuracy = 77.8%), with 12,13-DHOME being the most important differential metabolite in the model. The differential metabolic pathways between the two subtypes of IS patients included tricarboxylic acid (TCA) cycle, alanine, aspartate and glutamate metabolism, and pyruvate metabolism, mainly focused on energy metabolism. 12,13-DHOME emerged as the primary discriminatory metabolite between LAA and SVO subtypes of IS. In LAA subtype IS patients, energy metabolism, encompassing pyruvate metabolism and the TCA cycle, exhibited lower activity levels when compared to patients with the SVO subtype IS. The utilization of targeted metabolomics holds the potential to improve diagnostic accuracy for distinguishing stroke subtypes.

Biological characteristics of pregnancy in captive Yangtze finless porpoises revealed by urinary metabolomics†.

The Yangtze finless porpoises (Neophocaena asiaeorientalis a.) are an endemic and critically endangered species in China. Intensive captive breeding is essential for understanding the biology of critically endangered species, especially their pregnancy characteristics, knowledge of which is crucial for effective breeding management. Urine metabolomics can reveal metabolic differences, arising from physiological changes across pregnancy stages. Therefore, we used the urinary metabolomic technology, to explore urinary metabolite changes in pregnant Yangtze finless porpoises. A total of 2281 metabolites were identified in all samples, which including organic acids and derivatives (24.45%), organoheterocyclic compounds (20.23%), benzenoids (18.05%), organic oxygen compounds (7.73%), and phenylpropanoids and polyketides (6.48%). There were 164, 387, and 522 metabolites demonstrating differential abundance during early pregnancy, mid pregnancy, and late pregnancy, respectively, from the levels observed in nonpregnancy. The levels of pregnenolone, 17α-hydroxyprogesterone, and tetrahydrocortisone were significantly higher during all pregnancy stages, indicating their important roles in fetal development. The differential metabolites between nonpregnancy and pregnancy were mainly associated with amino acid and carbohydrate metabolism. Moreover, metabolic activity varied across pregnancy stages; steroid hormone biosynthesis was predominant in early pregnancy, and amino acid biosynthesis and carbohydrate metabolism were predominant in mid pregnancy and late pregnancy, respectively. Our results provide new insights into metabolic characteristics in the Yangtze finless porpoises' urine during pregnancy, and indicate that the differential levels of urine metabolites can determine pregnancy in Yangtze finless porpoises, providing valuable information for the husbandry and management of pregnant Yangtze finless porpoises in captivity.

Metabolomics Combined with Network Pharmacology to Explore the Active Components and Mechanism of Tetrastigma planicaule (Hook.) Gagnep. in the Treatment of Rheumatoid Arthritis

Context. Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease. It is characterized by persistent joint damage. Traditional Chinese medicine (TCM) has demonstrated notable efficacy in managing RA. Prior investigations have indicated that the ethyl acetate extract of Tetrastigma planicaule (Hook.) Gagnep. (TP) possesses substantial anti‐inflammatory properties, suggesting the potential for screening TCM drugs with antirheumatoid arthritis attributes. However, the precise mechanism underlying its pharmacological effects and material basis remains unclear, impeding the advancement of TCM innovation. Objective. This study is to elucidate the active components and mechanism of TP in the treatment of RA. Materials and Methods. A rat model of collagen‐induced arthritis (CIA) was established for conducting pharmacological experiments to assess the effectiveness of ethyl acetate extract from TP in treating RA. In addition, nuclear magnetic resonance (NMR) metabolomics technology was employed to identify potential endogenous biomarkers for further metabolic pathway analysis. The active compounds and key targets were investigated using ultraperformance liquid chromatography‐quadrupole time‐of‐flight mass spectrometry (UPLC‐Q‐TOF‐MS/MS) technology in combination with network pharmacology. Moreover, common gene targets discovered by metabolomics and network pharmacology were validated by molecular docking with the relevant active components. Result. 12 endogenous biomarkers were screened by 1H‐NMR metabolomics technology. The metabolite pathways are primarily implicated in lipid metabolism and amino acid metabolism. 49 compounds were identified in TP, of which 10 were considered active ingredients through network pharmacological analysis. In a comprehensive analysis, it was found that TP exhibited a strong association with the PLA2G4A and lipid metabolite pathways in RA. Molecular docking studies further demonstrated a high affinity between the active compounds of TP and PLA2G4A. Discussion and Conclusions. TP may play a therapeutic role in RA by regulating PLA2G4A and participating in back‐regulating the glycerophospholipid metabolic pathway. The study elucidated the multicomponent, multitarget, and multipathway mechanism of TP in the treatment of RA, laying the groundwork for a deeper understanding of its therapeutic mechanisms.