Metabonomics: a platform for studying drug toxicity and gene function

Multiscale metabolomics techniques: Insights into neuroscience research

The field of metabolomics examines the overall composition and dynamic patterns of metabolites in living organisms. The primary methods used in metabolomics include liquid chromatography (LC), nuclear magnetic resonance (NMR), and mass spectrometry (MS) analysis. These methods enable the identification and examination of metabolite types and contents within organisms, as well as modifications to metabolic pathways and their connection to the emergence of diseases. Research in metabolomics has extensive value in basic and applied sciences. The field of metabolomics is growing quickly, with the majority of studies concentrating on biomedicine, particularly early disease diagnosis, therapeutic management of human diseases, and mechanistic knowledge of biochemical processes. Multiscale metabolomics is an approach that integrates metabolomics techniques at various scales, including the holistic, tissue, cellular, and organelle scales, to enable more thorough and in-depth studies of metabolic processes in organisms. Multiscale metabolomics can be combined with methods from systems biology and bioinformatics. In recent years, multiscale metabolomics approaches have become increasingly important in neuroscience research due to the nervous system's high metabolic demands. Multiscale metabolomics can offer novel concepts and approaches for the diagnosis, treatment, and development of medication for neurological illnesses in addition to a more thorough understanding of brain metabolism and nervous system function. In this review, we summarize the use of multiscale metabolomics techniques in neuroscience, address the promise and constraints of these techniques, and provide an overview of the metabolome and its applications in neuroscience.

Effects of hypo-osmotic stress on osmoregulation, antioxidant response, and energy metabolism in sea cucumber Holothuria moebii under desalination environment

With global climate changing, hypo-salinity events are increasing in frequency and duration because of continuous rainfall and freshwater inflow, which causes reduced cytosolic osmolarity and cellular stress responses in aquatic animals. Sea cucumbers are considered stenohaline because they lack osmoregulatory organs and are vulnerable to salinity fluctuations. In this study, we performed multiple biochemical assays, de novo transcriptomics, and widely targeted metabolomics to comprehensively explore the osmoregulatory mechanisms and physiological responses of sea cucumber Holothuria moebii to hypo-osmotic stress, which is a representative specie that is frequently exposed to hypo-saline intertidal zones. Our results found that H. moebii contracted their ambulacral feet and oral tentacles, and the coelomic fluid ion concentrations were reduced to be consistent with the environment. The microvilli of intestines and respiratory trees underwent degeneration, and the cytoplasm exhibited swelling and vacuolation. Moreover, the Na+, K+, and Cl- concentrations and Na+/K+-ATPase activity were significantly reduced under hypo-osmotic stress. The decrease in protein kinase A activity and increase in 5'-AMP level indicated a significant inhibition of the cAMP signaling pathway to regulate ion concentrations. And small intracellular organic molecules (amino acids, nucleotides and their derivatives) also play crucial roles in osmoregulation through oxidative deamination of glutamate, nucleotide catabolism, and nucleic acid synthesis. Moreover, lysosomes and peroxisomes removed oxidative damage, whereas antioxidant metabolites, such as N-acetyl amino acids and glutathione, were increased to resist oxidative stress. With prolonged hypo-osmotic stress, glycerophospholipid metabolism was enhanced to maintain membrane stability. Furthermore, acyl-CoA-binding protein activity was significantly inhibited, and only a small amount of acylcarnitine was significantly accumulated, which indicated a disruption in energy metabolism. PPAR signaling pathway and choline content were up-regulated to promote fatty acid metabolism under hypo-osmotic stress. Overall, our results provide new insights into the osmoregulatory mechanisms and physiological responses of sea cucumbers to hypo-osmotic stress.

Combinatorial metabolomic and transcriptomic analysis of muscle growth in hybrid striped bass (female white bass Morone chrysops x male striped bass M. saxatilis)

BACKGROUND

Understanding growth regulatory pathways is important in aquaculture, fisheries, and vertebrate physiology generally. Machine learning pattern recognition and sensitivity analysis were employed to examine metabolomic small molecule profiles and transcriptomic gene expression data generated from liver and white skeletal muscle of hybrid striped bass (white bass Morone chrysops x striped bass M. saxatilis) representative of the top and bottom 10 % by body size of a production cohort.

RESULTS

Larger fish (good-growth) had significantly greater weight, total length, hepatosomatic index, and specific growth rate compared to smaller fish (poor-growth) and also had significantly more muscle fibers of smaller diameter (≤ 20 µm diameter), indicating active hyperplasia. Differences in metabolomic pathways included enhanced energetics (glycolysis, citric acid cycle) and amino acid metabolism in good-growth fish, and enhanced stress, muscle inflammation (cortisol, eicosanoids) and dysfunctional liver cholesterol metabolism in poor-growth fish. The majority of gene transcripts identified as differentially expressed between groups were down-regulated in good-growth fish. Several molecules associated with important growth-regulatory pathways were up-regulated in muscle of fish that grew poorly: growth factors including agt and agtr2 (angiotensins), nicotinic acid (which stimulates growth hormone production), gadd45b, rgl1, zfp36, cebpb, and hmgb1; insulin-like growth factor signaling (igfbp1 and igf1); cytokine signaling (socs3, cxcr4); cell signaling (rgs13, rundc3a), and differentiation (rhou, mmp17, cd22, msi1); mitochondrial uncoupling proteins (ucp3, ucp2); and regulators of lipid metabolism (apoa1, ldlr). Growth factors pttg1, egfr, myc, notch1, and sirt1 were notably up-regulated in muscle of good-growing fish.

CONCLUSION

A combinatorial pathway analysis using metabolomic and transcriptomic data collectively suggested promotion of cell signaling, proliferation, and differentiation in muscle of good-growth fish, whereas muscle inflammation and apoptosis was observed in poor-growth fish, along with elevated cortisol (an anti-inflammatory hormone), perhaps related to muscle wasting, hypertrophy, and inferior growth. These findings provide important biomarkers and mechanisms by which growth is regulated in fishes and other vertebrates as well.

Exploring the metabolomics profile of frailty- a systematic review

Background

Frailty is a multifaceted geriatric syndrome characterized by an increased vulnerability to stressful events. metabolomics studies are valuable tool for better understanding the underlying mechanisms of pathologic conditions. This review aimed to elucidate the metabolomics profile of frailty.

Method

This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) 2020 statement. A comprehensive search was conducted across multiple databases. Initially, 5027 results were retrieved, and after removing duplicates, 1838 unique studies were subjected to screening. Subsequently, 248 studies underwent full-text screening, with 21 studies ultimately included in the analysis. Data extraction was performed meticulously by two authors, and the quality of the selected studies was assessed using the Critical Appraisal Skills Program (CASP) checklist.

Results

The findings revealed that certain Branched-chain amino acids (BCAAs) levels were lower in frail subjects compared to robust subjects, while levels of glutamate and glutamine were higher in frail individuals. Moreover, sphingomyelins and phosphatidylcholines (PC) displayed a decreasing trend as frailty advanced. Additionally, other metabolic derivatives, such as carnitine, exhibited significant associations with frailty. These metabolites were primarily interconnected through biochemical pathways related to the tricarboxylic acid and urea cycles. Notably, frailty was associated with a decrease in metabolic derivatives, including carnitine.

Conclusion

This study underscores the intricate relationship between essential metabolites, including amino acids and lipids, and their varying levels in frail individuals compared to their robust counterparts. It provides a comprehensive panel of metabolites, shedding light on their potential associations with frailty and expanding our understanding of this complex syndrome.

Untargeted metabolomics reveals potential plasma biomarkers for diagnosis of primary aldosteronism using liquid chromatography-mass spectrometry

Metabolite profiling has the potential to comprehensively bridge phenotypes and complex heterogeneous physiological and pathological states. We performed a metabolomics study using parallel liquid chromatography-mass spectrometry (LC-MS) combined with multivariate data analysis to screen for biomarkers of primary aldosteronism (PA) from a cohort of 111 PA patients and 218 primary hypertension (PH) patients. Hydrophilic interaction chromatography and reversed-phase liquid chromatography separations were employed to obtain a global plasma metabolome of endogenous metabolites. The satisfactory classification between PA and PH patients was obtained using the MVDA model. A total of 35 differential metabolites were screened out and identified. A diagnostic biomarker panel was established using the least absolute shrinkage and selection operator (LASSO) binary logistic regression model and receiver operating characteristic analysis. Joint analysis with clinical indicators, including plasma supine aldosterone level, plasma orthostatic aldosterone level, body mass index, and blood potassium, revealed that the combination of metabolite biomarker panel and plasma supine aldosterone has the best clinical diagnostic efficacy.

MicroRNA-26a in respiratory diseases: mechanisms and therapeutic potential

MicroRNAs (miRNAs) are short, non-coding single-stranded RNA molecules approximately 22 nucleotides in length, intricately involved in post-transcriptional gene expression regulation. Over recent years, researchers have focused keenly on miRNAs, delving into their mechanisms in various diseases such as cancers. Among these, miR-26a emerges as a pivotal player in respiratory ailments such as pneumonia, idiopathic pulmonary fibrosis, lung cancer, asthma, and chronic obstructive pulmonary disease. Studies have underscored the significance of miR-26a in the pathogenesis and progression of respiratory diseases, positioning it as a promising therapeutic target. Nevertheless, several challenges persist in devising medical strategies for clinical trials involving miR-26a. In this review, we summarize the regulatory role and significance of miR-26a in respiratory diseases, and we analyze and elucidate the challenges related to miR-26a druggability, encompassing issues such as the efficiency of miR-26a, delivery, RNA modification, off-target effects, and the envisioned therapeutic potential of miR-26a in clinical settings.

Nontargeted metabolomics reveals sequential changes in amino acid and ferroptosis-related metabolism in Parkinson's disease

Parkinson's disease (PD) is inseparable from metabolic disorders but lacks assessment of specific metabolite alteration. To explore the sequential metabolic changes in PD progression, we evenly divided 78 C57BL/6 mice (10 weeks) into six groups (one control group and five experimental groups) and collected the hippocampus tissue of mice after treating with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, and probenecid (twice a week) at five periods (1, 2, 3, 4, and 5 weeks) for metabolome analysis. Our study identified 567 differentially abundant metabolites (DAMs) (total 4348 metabolites). Compared with controls, 145, 146, 171, 208, and 213 DAMs were obtained from the five experimental groups, respectively. Notably, 40 shared DAMs were present in five experimental groups, of which 22 shared DAMs formed a new metabolic network based on amino acid metabolism. Compared with group W3, 84 DAMs were identified in group W5, including 12 unique DAMs. DAMs in different stages of PD were significantly enriched in amino acid metabolism pathway, lipid metabolism pathway, and ferroptosis pathway. l-Glutamine, spermidine, and l-tryptophan were the key hubs in the whole metabolic process of PD. N-Formyl-l-methionine gradually increased in abundance with PD progression, whereas 5-methylcytosine gradually decreased. The study emphasized the sequential changes in DAMs in PD progression, stimulating subsequent studies.

Comprehensive profiling of amino acids and derivatives in biological samples: A robust UHPLC-MS/MS method for investigating acute lung injury

The severe respiratory dysfunctions associated with acute lung injury (ALI) and its sequelae have a high morbidity and mortality rate, are multifactorial, and lack a viable treatment. Considering the critical function that amino acids and derivatives play in the genesis of illnesses and the regulation of metabolic processes, monitoring the levels of metabolites associated with amino acids in biological matrices is necessary and interesting to study their pathological mechanisms. Exploring the dynamics of amino acids and derivatives level and searching for biomarkers provides improved clinical ideas for the diagnosis and treatment of ALI. Therefore, we developed an ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS) method that can simultaneously determine the amino acid and derivatives metabolic levels to study amino acid profiles in different biological samples to facilitate clinical research of ALI. In this study, 48 amino acids and derivatives, including neurotransmitters, polyamines, purines, and other types, were quantified simultaneously in a fast, high-throughput, sensitive, and reliable manner within a 15-minute run time without derivatization. No relevant studies have been reported to quantify these 48 amino acid metabolites in three biological samples simultaneously. Satisfactory linearity (R > 0.995), inter-day and intra-day accuracy (85.17-112.67 % and 85.29-111.60 %, respectively), inter-day and intra-day precision (RSD < 13.80 % and RSD < 12.01 %, respectively), matrix effects (81.00 %-118.00 %), recovery (85.09 %-114.65 %) and stability (RSD < 14.72 %) were all demonstrated by the optimized method's successful validation for all analytes. In addition, the suggested method was effectively implemented in plasma, urine, and lung tissue from normal mice and mice with ALI, with the aim of finding potential biomarkers associated with ALI. Potential biomarkers were screened through multivariate statistical analysis and volcanic map analysis, and the changes of markers in ALI were again identified through heat map analysis and correlation analysis with biochemical indicators, which provided ideas and references for subsequent mechanism studies. Here, the technique created in this work offers a quick and dependable way to perform an integrated analysis of amino acids in a variety of biological materials, which can provide research ideas for understanding the physiopathological state of various diseases.

The safety evaluation of Shenze Shugan capsule and mechanism of apoptosis induced by five potentially nephrotoxic components

ETHNOPHARMACOLOGICAL RELEVANCE

Shenze Shugan capsule is a prescription of traditional Chinese medicine for nonalcoholic steatohepatitis treatment. It includes Rhei Radix et Rhizoma (RR), Cassiae Semen (CS) and Alismatis Rhizoma(AR), which widely contains rhein, emodin, aurantio-obtusin, alisol A and alisol B 23-monoacetate.

AIM OF THE STUDY

In this study, we aimed to explore the safety of the medicine, and further elucidate the mechanism of apoptosis induction in HK-2 cells by five components, including rhein, emodin, aurantio-obtusin, alisol A and alisol B 23-monoacetate.

MATERIALS AND METHODS

We investigated the nephrotoxicity of Shenze Shugan capsule, including RR, CS, AR and mixed herbs given for two months in rats. Superoxide dismutase (SOD) in kidney tissues, urea nitrogen (BUN) and creatinine (CRE) in serum were detected, and renal pathology analysis was performed. In cell experiments, the apoptotic rate and cell cycle distribution of HK-2 cells were tested by flow cytometry. The levels of mitochondrial membrane potential (ΔΨm) and related protein expression in mitochondrial pathway were measured as well.

RESULTS

We confirmed that two months of administering high doses(60 times the dose for clinical use in adults) of RR, CS or mixed herbs upregulated the levels of CRE and RUN, inhibited SOD activity, and increased the degree of tubular degeneration and glomerular dilatation, but Shenze Shugan capsule has no significant differences in renal structure or renal function. In addition, we found that five components all concentration-dependently inhibited HK-2 cells proliferation and induced apoptosis, especially aurantio-obtusin as the novel nephrotoxic component. Rhein and emodin significantly induced S/M accumulation, but aurantio-obtusin, alisol A and alisol B 23-monoacetate significantly induced G1/M accumulation in HK-2 cells. Similarly, they could induce Caspase3 activation, loss of mitochondrial membrane potential (ΔΨm), and down-regulation of Bcl-2 and up-regulation of Bax.

CONCLUSIONS

Through a two-month subchronic toxicity study in rats, our preliminary determination is that this formulation is safe and reliable for long-term use. Interestingly, the potentially toxic herbs such as RR, CS, AR can reduce toxicity by drug compatibility. When further exploring the mechanism of action of toxic herbs, we found that mitochondrial pathway is involved in the apoptosis of HK -2 cells induced by rhein, emodin, aurantio-obtusin, alisol A and alisol B 23-monoacetate. Our findings provide new ideas for safety studies of Shenze Shugan capsule.

Critical Review of Selected Analytical Platforms for GC-MS Metabolomics Profiling-Case Study: HS-SPME/GC-MS Analysis of Blackberry's Aroma

Data processing and data extraction are the first, and most often crucial, steps in metabolomics and multivariate data analysis in general. There are several software solutions for these purposes in GC-MS metabolomics. It becomes unclear which platform offers what kind of data and how that information influences the analysis's conclusions. In this study, selected analytical platforms for GC-MS metabolomics profiling, SpectConnect and XCMS as well as MestReNova software, were used to process the results of the HS-SPME/GC-MS aroma analyses of several blackberry varieties. In addition, a detailed analysis of the identification of the individual components of the blackberry aroma club varieties was performed. In total, 72 components were detected in the XCMS platform, 119 in SpectConnect, and 87 and 167 in MestReNova, with automatic integral and manual correction, respectively, as well as 219 aroma components after manual analysis of GC-MS chromatograms. The obtained datasets were fed, for multivariate data analysis, to SIMCA software, and underwent the creation of PCA, OPLS, and OPLS-DA models. The results of the validation tests and VIP-pred. scores were analyzed in detail.

Toxic effects and action mechanism of metal-organic framework UiO-66-NH2 in Microcystisaeruginosa

The zirconium metal-organic framework UiO-66-NH2 has garnered considerable attention for their potentials of removing environmental contaminants from water. The production and application of UiO-66-NH2 make their releases into the aquatic environment inevitable. Nevertheless, little information is available regarding its potential risk to the environment and aquatic organisms, thus limiting the evaluation of its safe and sustainable use. In this study, the ecotoxicity of UiO-66-NH2 was evaluated, specifically its impacts on growth, extracellular organic matter release, and metabolomic changes of the model phytoplankton Microcystis aeruginosa (M. aeruginosa). UiO-66-NH2 exhibited moderate effects on algal physiology including growth, viability, and photosynthetic system. At concentrations below 20 mg/L, UiO-66-NH2 induced negligible inhibition of algal growth, algal viability, and photosynthesis. In contrast, UiO-66-NH2 boosted the release of extracellular organic matter even at concentration as low as 0.02 mg/L. These findings indicated that, while no evident damage to algal cells was observed, UiO-66-NH2 was hazardous to the aquatic environment as it stimulated the release of algal toxins. Moreover, UiO-66-NH2 entered algal cells rather than adhering to the surface of M. aeruginosa as observed by the fluorescence imaging. Based on metabolic analysis, UiO-66-NH2 influenced the cyanobacteria mainly through interference with purine metabolism and ABC transporter. This study sheds light on the potential threat UiO-66-NH2 posing to microalgae, and has potential implications for its safe utilization in the environmental field.

High-throughput omics technologies in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.

Neuroprotective mechanisms of defatted walnut powder against scopolamine-induced Alzheimer's disease in mice revealed through metabolomics and proteomics analyses

ETHNOPHARMACOLOGICAL RELEVANCE

Defatted walnut powder (DWP), the byproduct remaining after extracting oil from the walnut kernel, has the actions of nourishing liver and the kidney, replenishing blood, and calming the nerves, which is believed to be a brain-nourishing in Chinese medicine. DWP is rich in phenolic substances with demonstrated anti-inflammatory, antioxidant, lipid-lowering and neuroprotective effects. Despite these promising properties of DWP, its effectiveness in treating Alzheimer's disease (AD) remains unclear, and further research is needed to understand the mechanism of action.

AIM OF THE STUDY

This study aimed to investigate the potential mechanism of DWP on AD by constructing the overall metabolic profile of mice with an anti-scopolamine AD model and verification of the highly correlated pathway.

MATERIALS AND METHODS

The neuroprotective efficacy of DWP in a mouse model of AD established by scopolamine injection was examined. Spatial memory performance in the Morris water maze (MWM), markers of cholinergic function in hippocampus and cortex, and neuropathological changes were compared among control, model, and DWP-consuming model group mice. In addition, combined metabolomic and proteomic analyses were conducted to investigate changes in metabolite and protein expression profiles in AD model mice induced by DWP consumption. Differentially expressed proteins and metabolites were then analyzed for KEGG pathway enrichment and results confirmed through targeted amino acid metabolomics.

RESULTS

The results showed that consumption of DWP improved spatial learning and memory in the MWM, enhanced cholinergic function, and reduced histopathological damage in the cortex and hippocampus of AD model mice. Based on differentially abundant metabolites and proteins, 43 metabolic pathways modulated by DWP were identified, mainly involving in amino acid metabolic pathways strongly associated with cellular energetics and antioxidant capacity, and targeted amino acid metabolomics confirmed that DWPE significantly elevated the levels of Arginine (Arg), Histidine (His), Proline (Pro), Serine (Ser), and Tyrosine (Tyr), while reducing the levels of Glutamate (Glu). This ultimately resulted in an improvement in the progression of AD.

CONCLUSION

This study identified numerous metabolic networks modulated by DWP that can mitigate scopolamine-induced AD neuropathology and cognitive dysfunction. DWP is a promising resource to identify AD-related pathogenic pathways and therapeutic strategies.

A new insight into mechanism of colchicine poisoning based on untargeted metabolomics

BACKGROUND

Colchicine (COL) is a well-known plant-derived mitogenic toxin that has been widely applied for the treatment of immune system diseases and various cancers. However, its clinical use is severely limited by frequent occurrence of poisoning accidents, and the mechanism of COL poisoning is not clear yet.

PURPOSE

The present study aimed to unveil how COL works as a toxin based on untargeted metabolomics analysis of animal models and clinical human case.

METHODS

KM mice orally administered COL were used to establish poisoning models, and plasma samples were collected for untargeted metabolomics analysis. The data mining was performed to screen dose-dependent differences and disturbed metabolic pathways. The blood samples collected from clinical COL poisoning human case at various time points during treatment period were further analyzed to investigate the temporal changes in the metabolic disposition of COL in vivo and also verify the findings from mice. Finally, the expression of key pathways was evaluated by ELISA and Western blotting analysis.

RESULTS

Histological examination demonstrated systemic toxicity of COL poisoning in mice. Metabolite profiling analysis of plasma samples from model mice and clinical case both revealed that COL poisoning could significantly disturb in vivo metabolism of amino acid and lipid metabolism by the FXR/AMPK signal pathway. Quantitative monitoring of the metabolic process of COL further demonstrated that it could be greatly ameliorated with the rapid metabolic transformation of COL in vivo, which thus may be an effective detoxification pathway for COL poisoning.

CONCLUSION

The findings of the present study provided new insight into the molecular mechanism of COL poisoning, thus helpful for guiding reasonable application of this phytotoxin.

The metabolic fingerprint of chronic hepatitis C progression: Metabolome shifts and cutting-edge diagnostic options

Hepatitis C virus infection causes chronic diseases such as cirrhosis and hepatocellular carcinoma. Metabolomics research has been shown to be linked to pathophysiologic pathways in liver illnesses. The aim of this study was to investigate the serum metabolic profile of patients with chronic hepatitis C (CHC) infection and to identify underlying mechanisms as well as potential biomarkers associated with the disease. Nuclear magnetic resonance (NMR) was used to evaluate the sera of 83 patients with CHC virus and 52 healthy control volunteers (NMR). Then, multivariate statistical analysis was used to find distinguishing metabolites between the two groups. Sixteen out of 40 metabolites including include 3-HB, betaine, carnitine, creatinine, fucose, glutamine, glycerol, isopropanol, lysine, mannose, methanol, methionine, ornithine, proline, serine, and valine-were shown to be significantly different between the CHC and normal control (NC) groups (variable importance in projection >1 and p < 0.05). All the metabolic perturbations in this disease are associated with pathways of Glycine, serine, and threonine metabolism, glycerolipid metabolism, arginine and proline metabolism, aminoacyl-tRNA biosynthesis, cysteine and methionine metabolism, alanine, aspartate, and glutamate metabolism. Multivariate statistical analysis constructed using these expressed metabolites showed CHC patients can be discriminated from NCs with high sensitivity (90%) and specificity (99%). The metabolomics approach may expand the diagnostic armamentarium for patients with CHC while contributing to a comprehensive understanding of disease mechanisms.

Metabolome and Transcriptome Association Analysis Reveals the Link Between Pigmentation and Nutrition Utilization in the Juveniles of Sea Cucumber Holothuria leucospilota

The sea cucumber Holothuria leucospilota is an economically and ecologically important tropical species. Following development into juveniles, H. leucospilota undergoes a color change from white to black, involving a pigmentation process for over a period of several months. In this study, a combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and Next-Generation sequencing (NGS) were employed to investigate the changes in metabolomic and transcriptomic profiles during pigmentation in H. leucospilota juveniles. The metabolomic analysis identified a total of 341 metabolites, of which 52 were found to be differentially regulated (P < 0.05 and VIP > 1), with 27 being upregulated in white individuals and 25 in black individuals. Additionally, 632 differentially expressed genes (DEGs) were identified, with 380 genes upregulated in white samples and 252 genes upregulated in black samples. Interestingly, the melanin content and tyrosinase transcript levels did not display significant differences between the two groups. Metabolomic data suggested the involvement of the linoleic acid metabolic pathway in pigmentation. Transcriptomic analysis, coupled with realtime PCR validation, revealed a decrease in the transcript levels of digestive enzymes like α-amylase, maltase-glucoamylase, and trehalase after the juveniles changed to black. Furthermore, the mRNA expressions of major yolk proteins showed a decline, indicating a shift in the accumulation of protein nutrient sources. Overall, our findings suggest that during the pigmentation process in H. leucospilota, no significant changes were observed in the classical melanin pathway, while notable alterations were observed in their nutritional status. This study provides valuable insights into the regulatory mechanisms of pigmentation in marine organisms.

Comparative metabolomics analysis investigating the impact of melatonin-enriched diet on energy metabolism in the crayfish, Cherax destructor

Melatonin is a multifunctional bioactive molecule present in almost all organisms and has been gradually used in the aquaculture industry in recent years. Energy metabolism is an essential process for individuals to maintain their life activities; however, the process through which melatonin regulates energy metabolism in aquatic animals remains unclear. The present study aimed to conduct a comprehensive analysis of the regulatory mechanism of melatonin for energy metabolism in Cherax destructor by combining metabolomics analysis with the detection of the key substance content, enzymatic activity, and gene expression levels in the energy metabolism process after culturing with dietary melatonin supplementation for 8 weeks. Our results showed that dietary melatonin increased the content of glycogen, triglycerides, and free fatty acids; decreased lactate levels; and promoted the enzymatic activity of pyruvate kinase (PK), malate dehydrogenase (MDH), and acetyl-CoA carboxylase. The results of gene expression analysis showed that dietary melatonin also increased the expression levels of hexokinase, PK, MDH, lactate dehydrogenase, lipase, and fatty acid synthase genes. The results of metabolomics analysis showed that differentially expressed metabolites were significantly enriched in lysine degradation and glycerophospholipid metabolism. In conclusion, our study demonstrates that dietary melatonin increased oxidative phosphorylation, improved glucose utilization, and promoted storage of glycogen and lipids in C. destructor. These lipids are used not only for energy storage but also to maintain the structure and function of cell membranes. Our results further add to the understanding of the mechanisms of energy regulation by melatonin in crustaceans.

Optimising a urinary extraction method for non-targeted GC-MS metabolomics

Urine is ideal for non-targeted metabolomics, providing valuable insights into normal and pathological cellular processes. Optimal extraction is critical since non-targeted metabolomics aims to analyse various compound classes. Here, we optimised a low-volume urine preparation procedure for non-targeted GC-MS. Five extraction methods (four organic acid [OA] extraction variations and a "direct analysis" [DA] approach) were assessed based on repeatability, metabolome coverage, and metabolite recovery. The DA method exhibited superior repeatability, and achieved the highest metabolome coverage, detecting 91 unique metabolites from multiple compound classes comparatively. Conversely, OA methods may not be suitable for all non-targeted metabolomics applications due to their bias toward a specific compound class. In accordance, the OA methods demonstrated limitations, with lower compound recovery and a higher percentage of undetected compounds. The DA method was further improved by incorporating an additional drying step between two-step derivatization but did not benefit from urease sample pre-treatment. Overall, this study establishes an improved low-volume urine preparation approach for future non-targeted urine metabolomics applications using GC-MS. Our findings contribute to advancing the field of metabolomics and enable efficient, comprehensive analysis of urinary metabolites, which could facilitate more accurate disease diagnosis or biomarker discovery.

Investigating the relationship between non-occupational pesticide exposure and metabolomic biomarkers

The relationship between pesticide exposures and metabolomics biomarkers is not well understood. We examined the changes in the serum metabolome (early biomarkers) and the metabolic pathways associated with various pesticide exposure scenarios (OPE: overall exposure, PEM: exposure in months, PEY: exposure in years, and PEU: reported specific pesticides use) using data from the Northern Finland Birth Cohort 1966 31-year cross-sectional examination. We utilized questionnaire data on pesticide exposures and serum samples for nuclear magnetic resonance (NMR)-based metabolomics analyses. For exposures and metabolites associations, participants size varied between 2,361 and 5,035. To investigate associations between metabolomics biomarkers and exposure to pesticide scenarios compared to those who reported no exposures multivariable regression analyses stratified by sex and adjustment with covariates (season of pesticide use, socioeconomic position (SEP), alcohol consumption, BMI, and latitude of residence) were performed. Multiple testing by Benjamini-Hochberg false discovery rate (FDR) correction applied. Pesticide exposures differed by sex, season of pesticide use, alcohol, SEP, latitude of residence. Our results showed that all pesticide exposure scenarios were negatively associated with decreased HDL concentrations across all lipoprotein subclasses in women. OPE, PEY, and PEU were associated with decreased branched-chain amino acid concentrations in men and decreased albumin concentrations in women. OPE, PEY and PEU were also associated with changes in glycolysis metabolites and ketone bodies in both sexes. Specific pesticides exposure was negatively associated with sphingolipids and inflammatory biomarkers in men. In women, OPE, PEM, and PEU were associated with decreased apolipoprotein A1 and increased apolipoprotein B/apolipoprotein A1 ratio. Our findings suggest that identification of early biomarkers of disease risk related to pesticide exposures can inform strategies to reduce exposure and investigate causal pathways. Women may be more susceptible to non-occupational pesticide exposures when compared to men, and future sex-specific studies are warranted.

Probing organoid metabolism using fluorescence lifetime imaging microscopy (FLIM): The next frontier of drug discovery and disease understanding

Organoid models have been used to address important questions in developmental and cancer biology, tissue repair, advanced modelling of disease and therapies, among other bioengineering applications. Such 3D microenvironmental models can investigate the regulation of cell metabolism, and provide key insights into the mechanisms at the basis of cell growth, differentiation, communication, interactions with the environment and cell death. Their accessibility and complexity, based on 3D spatial and temporal heterogeneity, make organoids suitable for the application of novel, dynamic imaging microscopy methods, such as fluorescence lifetime imaging microscopy (FLIM) and related decay time-assessing readouts. Several biomarkers and assays have been proposed to study cell metabolism by FLIM in various organoid models. Herein, we present an expert-opinion discussion on the principles of FLIM and PLIM, instrumentation and data collection and analysis protocols, and general and emerging biosensor-based approaches, to highlight the pioneering work being performed in this field.

Metabolomics and lipidomics strategies in modern drug discovery and development

Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.

CDCT-induced nephrotoxicity in rat by apoptosis via metabolic disturbance

Compound diclofenac sodium chlorphenamine maleate tablets (CDCT) are widely used for the cold in Asia. However, CDCT can cause hematuria symptoms in clinical, and the underlying mechanism is unknown. This study aims to investigate the CDCT-induced changes of morphology in kidney and metabolites and further explore the possible mechanisms of CDCT-induced nephrotoxicity. Sprague-Dawley rats were exposed to the CDCT at a clinical equivalent dose for 6 days. CDCT exposure can induce kidney injury and death. Pathological changes, including creatinine, urea nitrogen, and histopathology, were observed in rats. Furthermore, metabolomic-driven energy and glycerophospholipid metabolism pathway disorders, accompanied by remarkably changed key metabolites, such as succinate, leukotriene B4 (LTB4 ), and cardiolipin (CL), are observed in the CDCT-induced nephrotoxicity. Functionally, succinate accumulation leads to mitochondrial damage, as evidence by the imbalance of complex I and complex II and an increase in mitochondrial reactive oxygen species (mito SOX). Meanwhile, LTB4 activated the NF-κB signaling, as shown by increased protein of p65, phosphor-p65, and decreased protein of IκBα and phosphor-IκBα. Eventually, the apoptosis pathway was triggered in response to reduced CL, inflammation, and mito SOX, as demonstrated by the expression of cyt c, Bax, Bcl-2, caspase-3, and caspase-9. This study indicated that CDCT-induced metabolic disorders triggered nephrotoxicity and provided a comprehensive information to elucidate the mechanism of CDCT induced nephrotoxicity.

Association of Plasma Selenium and Its Untargeted Metabolomic Profiling with Cervical Cancer Prognosis

Selenium is an essential trace element that shows beneficial or adverse health effects depending on the dose. However, its role in the prognosis of cervical cancer (CC) has been less reported. We aimed to explore the association between selenium status and prognosis in CC patients with different prognoses and to elucidate the underlying mechanism of selenium in CC prognosis. This cross-sectional observational study had a case-control design at the Harbin Medical University Cancer Hospital and was conducted using 29 CC cases with poor prognosis and 29 CC cases with good prognosis. Plasma selenium levels were measured using an atomic fluorescence spectrometer. Untargeted metabolomics was used to identify metabolites. Plasma selenium levels of the poor prognosis group (49.90 ± 13.81 µg/L) were lower than that of the good prognosis group (59.38 ± 13.00 µg/L, t = 2.69, P = 0.009). In the logistic regression analysis, plasma selenium levels were associated with lower poor prognosis risk [odds ratio (OR) = 0.952, 95% CI: 0.909-0.998]. Receiver operating characteristic curve analysis revealed an optimal cut-off point of plasma selenium levels ≤ 47.68 µg/L for poor prognosis of CC. Based on the cut-off selenium levels, patients with different prognoses were divided into high and low selenium groups. Metabolomic analysis revealed six differential metabolites among different prognoses with low and high selenium levels, and the glycerophospholipid (GPL) metabolism was enriched. Plasma selenium levels were positively correlated with metabolite levels. Our findings provided evidence that low plasma selenium levels may associate with a poor prognosis of CC. Low plasma selenium levels might suppress GPL metabolism and influence the prognosis of CC. This finding requires confirmation in future prospective cohort studies.

Sardinian Infants of Diabetic Mothers: A Metabolomics Observational Study

Gestational diabetes mellitus (GDM) is a condition characterized by glucose intolerance, with hyperglycemia of varying severity with onset during pregnancy. An uncontrolled GDM can lead to an increased risk of morbidity in the fetus and newborn, and an increased risk of obesity or developing type 2 diabetes, hypertension or neurocognitive developmental impairment in adulthood. In this study, we used nuclear magnetic resonance (NMR) spectroscopy and gas chromatography-mass spectrometry (GS-MS) to analyze the urinary metabolomic profile of newborns of diabetic mothers (NDMs) with the aim of identifying biomarkers useful for the monitoring of NDMs and for early diagnosis of predisposition to develop related chronic diseases. A total of 26 newborns were recruited: 21 children of diabetic mothers, comprising 13 in diet therapy (NDM-diet) and 8 in insulin therapy (NDM-insulin), and 5 control children of non-diabetic mothers (CTR). Urine samples were collected at five time points: at birth (T1), on the third day of life (T2), one week (T3), one month (T4) and six months postpartum (T5). At T1, variations were observed in the levels of seven potential biomarkers (acetate, lactate, glycylproline/proline, isocitrate, N,N-dimethylglycine, N-acetylglucosamine and N-carbamoyl-aspartate) in NMD-insulin infants compared to NDM-diet and CTR infants. In particular, the altered metabolites were found to be involved in several metabolic pathways such as citrate metabolism, glycine, serine and threonine metabolism, arginine and proline metabolism, amino sugar and nucleotide sugar metabolism, and pyruvate metabolism. In contrast, these changes were not visible at subsequent sampling times. The impact of early nutrition (maternal and formula milk) on the metabolomic profile was considered as a potential contributing factor to this finding.

Metabolomics Approaches for the Diagnosis, Treatment, and Better Disease Management of Viral Infections

Metabolomics is an analytical approach that involves profiling and comparing the metabolites present in biological samples. This scoping review article offers an overview of current metabolomics approaches and their utilization in evaluating metabolic changes in biological fluids that occur in response to viral infections. Here, we provide an overview of metabolomics methods including high-throughput analytical chemistry and multivariate data analysis to identify the specific metabolites associated with viral infections. This review also focuses on data interpretation and applications designed to improve our understanding of the pathogenesis of these viral diseases.

Elemene induces cell apoptosis via inhibiting glutathione synthesis in lung adenocarcinoma

ETHNOPHARMACOLOGICAL RELEVANCE

The rhizome of Curcuma wenyujin Y.H. Chen & C. Ling, also known as Wen-E-Zhu, has been used for cancer treatment since ancient times, with roots dating back to the Song Dynasty. Elemene (EE), a sesquiterpene extract with potent anticancer properties, is extracted from Wen-E-Zhu, with β-elemene (BE) being its main active compound, along with trace amounts of β-caryophyllene (BC), γ-elemene and δ-elemene isomers. EE has demonstrated broad-spectrum anti-cancer effects and is commonly used in clinical treatments for various types of malignant cancers, including lung cancer. Studies have shown that EE can arrest the cell cycle, inhibit cancer cell proliferation, and induce apoptosis and autophagy. However, the exact mechanism of its anti-lung cancer activity remains unclear and requires further research and investigation.

AIM OF THE STUDY

In this study, the possible mechanism of EE and its main active components, BE and BC, against lung adenocarcinoma was investigated by using A549 and PC9 cell lines.

MATERIALS AND METHODS

The subcutaneous tumor model of nude mice was constructed to evaluate the efficacy of EE in vivo, then the in vitro half-inhibitory concentration (IC₅₀) of EE and its main active components, BE and BC, on A549 and PC9 cells at different concentrations were determined by CCK-8. Flow cytometry was used to detect the apoptosis and cycle of A549 and PC9 cells treated with different concentrations of BE and BC for 24 h. Non-targeted metabolomics analysis was performed on A549 cells to explore potential target pathways, which were subsequently verified through kit detection and western blot analysis.

RESULTS

Injection of EE in A549 tumor-bearing mice effectively suppressed cancer growth in vivo. The IC₅₀ of EE and its main active components, BE and BC, was around 60 μg/mL. Flow cytometry analysis showed that BE and BC blocked the G₂/M and S phases of lung adenocarcinoma cells and induced apoptosis, leading to a significant reduction in mitochondrial membrane potential (MMP). Results from non-targeted metabolomics analysis indicated that the glutathione metabolism pathway in A549 cells was altered after treatment with the active components. Kit detection revealed a decrease in glutathione (GSH) levels and an increase in the levels of oxidized glutathione (GSSG) and reactive oxygen (ROS). Supplementation of GSH reduced the inhibitory activity of the active components on lung cancer and also decreased the ROS content of cells. Analysis of glutathione synthesis-related proteins showed a decrease in the expression of glutaminase, cystine/glutamate reverse transporter (SLC7A11), and glutathione synthase (GS), while the expression of glutamate cysteine ligase modified subunit (GCLM) was increased. In the apoptosis-related pathway, Bax protein and cleaved caspase-9/caspase-9 ratio were up-regulated and Bcl-2 protein was down-regulated.

CONCLUSIONS

EE, BE, and BC showed significant inhibitory effects on the growth of lung adenocarcinoma cells, and the mechanism of action was linked to the glutathione system. By down-regulating the expression of proteins related to GSH synthesis, EE and its main active components BE and BC disrupted the cellular redox system and thereby promoted cell apoptosis.

Metabolic changes in the plasma of mild Alzheimer's disease patients treated with Hachimijiogan

Background: Alzheimer's disease (AD), the most prevalent form of dementia, is a debilitating, progressive neurodegeneration. Amino acids play a wide variety of physiological and pathophysiological roles in the nervous system, and their levels and disorders related to their synthesis have been related to cognitive impairment, the core feature of AD. Our previous multicenter trial showed that hachimijiogan (HJG), a traditional Japanese herbal medicine (Kampo), has an adjuvant effect for Acetylcholine estelase inhibitors (AChEIs) and that it delays the deterioration of the cognitive dysfunction of female patients with mild AD. However, there are aspects of the molecular mechanism(s) by which HJG improves cognitive dysfunction that remain unclear. Objectives: To elucidate through metabolomic analysis the mechanism(s) of HJG for mild AD based on changes in plasma metabolites. Methods: Sixty-seven patients with mild AD were randomly assigned to either an HJG group taking HJG extract 7.5 g/day in addition to AChEI or to a control group treated only with AChEI (HJG:33, Control:34). Blood samples were collected before, 3 months, and 6 months after the first drug administration. Comprehensive metabolomic analyses of plasma samples were done by optimized LC-MS/MS and GC-MS/MS methods. The web-based software MetaboAnalyst 5.0 was used for partial least square-discriminant analysis (PLS-DA) to visualize and compare the dynamics of changes in the concentrations of the identified metabolites. Results: The VIP (Variable Importance in Projection) score of the PLS-DA analysis of female participants revealed a significantly higher increase in plasma metabolite levels after HJG administration for 6 months than was seen in the control group. In univariate analysis, the aspartic acid level of female participants showed a significantly higher increase from baseline after HJG administration for 6 months when compared with the control group. Conclusion: Aspartic acid was a major contributor to the difference between the female HJG and control group participants of this study. Several metabolites were shown to be related to the mechanism of HJG effectiveness for mild AD.

Active post-transcriptional regulation and ACLY-mediated acetyl-CoA synthesis as a pivotal target of Shuang-Huang-Sheng-Bai formula for lung adenocarcinoma treatment

BACKGROUND

New therapeutic approaches are required to improve the outcomes of lung cancer (LC), a leading cause of cancer-related deaths worldwide. Chinese herbal medicine formulae widely used in China provide a unique opportunity for improving LC treatment, and the Shuang-Huang-Sheng-Bai (SHSB) formula is a typical example. However, the underlying mechanisms of action remains unclear.

PURPOSE

This study aimed to confirm the efficacy of SHSB against lung adenocarcinoma (LUAD), which is a major histological type of LC, unveil the downstream targets of this formula, and assess the clinical relevance and biological roles of the newly identified target.

METHODS

An experimental metastasis mouse model and a subcutaneous xenograft mouse model were used to evaluate the anti-cancer activity of SHSB. Multi-omics profiling of subcutaneous tumors and metabolomic profiling of sera were performed to identify downstream targets, especially the metabolic targets of SHSB. A clinical trial was conducted to verify the newly identified metabolic targets in patients. Next, the metabolites and enzymes engaged in the metabolic pathway targeted by SHSB were measured in clinical samples. Finally, routine molecular experiments were performed to decipher the biological functions of the metabolic pathways targeted by SHSB.

RESULTS

Oral SHSB administration showed overt anti-LUAD efficacy as revealed by the extended overall survival of the metastasis model and impaired growth of implanted tumors in the subcutaneous xenograft model. Mechanistically, SHSB administration altered protein expression in the post-transcriptional layer and modified the metabolome of LUAD xenografts. Integrative analysis demonstrated that SHSB markedly inhibited acetyl-CoA synthesis in tumors by post-transcriptionally downregulating ATP-citrate lyase (ACLY). Consistently, our clinical trial showed that oral SHSB administration declined serum acetyl-CoA levels of patients with LC. Moreover, acetyl-CoA synthesis and ACLY expression were both augmented in clinical LUAD tissues of patients, and high intratumoral ACLY expression predicted a detrimental prognosis. Finally, we showed that ACLY-mediated acetyl-CoA synthesis is essential for LUAD cell growth by promoting G1/S transition and DNA replication.

CONCLUSION

Limited downstream targets of SHSB for LC treatment have been reported in previous hypothesis-driven studies. In this study, we conducted a comprehensive multi-omics investigation and demonstrated that SHSB exerted its anti-LUAD efficacy by actively and post-transcriptionally modulating protein expression and particularly restraining ACLY-mediated acetyl-CoA synthesis.

Amino acid analysis as a method of discovering biomarkers for diagnosis of diabetes and its complications

Diabetes mellitus (DM) is a severe chronic diseases with a global prevalence of 9%, leading to poor health and high health care costs, and is a direct cause of millions of deaths each year. The rising epidemic of diabetes and its complications, such as retinal and peripheral nerve disease, is a huge burden globally. A better understanding of the molecular pathways involved in the development and progression of diabetes and its complications can facilitate individualized prevention and treatment. High diabetes mellitus incidence rate is caused mainly by lack of non-invasive and reliable methods for early diagnosis, such as plasma biomarkers. The incidence of diabetes and its complications in the world still grows so it is crucial to develop a new, faster, high specificity and more sensitive diagnostic technologies. With the advancement of analytical techniques, metabolomics can identify and quantify multiple biomarkers simultaneously in a high-throughput manner, and effective biomarkers can greatly improve the efficiency of diabetes and its complications. By providing information on potential metabolic pathways, metabolomics can further define the mechanisms underlying the progression of diabetes and its complications, help identify potential therapeutic targets, and improve the prevention and management of T2D and its complications. The application of amino acid metabolomics in epidemiological studies has identified new biomarkers of diabetes mellitus (DM) and its complications, such as branched-chain amino acids, phenylalanine and arginine metabolites. This study focused on the analysis of metabolic amino acid profiling as a method for identifying biomarkers for the detection and screening of diabetes and its complications. The results presented are all from recent studies, and in all cases analyzed, there were significant changes in the amino acid profile of patients in the experimental group compared to the control group. This study demonstrates the potential of amino acid profiles as a detection method for diabetes and its complications.

Magnetic resonance spectroscopy ex vivo: A short historical review

Over the last half century, there have been several periods during which magnetic resonance spectroscopy (MRS) has been used ex vivo, for a variety of reasons, on samples such as microorganisms, cells, animal or human tissue, tissue extracts or biological fluids. These studies began in the days before the acronym MRS had been invented, when all such methods were still called nuclear magnetic resonance (NMR), and have extended to the present day. I will describe the historical development of NMR methods used ex vivo, their influences on the development of MRS in vivo, and their longer-term uses. All the interpretations will be personal, based on what I saw, or discussed with colleagues at the time.

Integration of serum metabolomics and network pharmacology reveals the immunoenhancing mechanisms of Qishenbuqi capsules

Introduction

Qishenbuqi capsule (QSBQC), a listed Chinese patent prescription, comprises of 4 herbs. Clinically, it has been shown to improve immune functions.

Methods

Subjects with Qi deficiency and non-Qi deficiency were recruited, who then took QSBQC for 4 weeks. Traditional Chinese medicine (TCM) syndrome scores and the levels of white blood cells, CD3+ T cells (CD3+), CD4+ T cells (CD3+CD4+), CD8+ T cells (CD3+CD8+), and CD4+/CD8+ were determined. Serum metabolomics was used to explore the metabolic mechanisms of QSBQC on improving immunity. Meanwhile, the potential active ingredients, targets, and pathways of QSBQC on enhancing immunity were screened by network pharmacology.

Results

QSBQC significantly improved TCM syndrome scores and increased the number of CD8+ T cells of both Qi deficiency and non-Qi deficiency subjects. Serum metabolomics revealed that QSBQC regulated 18 differential metabolites and 8 metabolic pathways of Qi deficiency, and 12 differential metabolites and 7 metabolic pathways of non-Qi deficiency subjects. The "herbs-compounds-pathways" diagram showed that PQ-2, cimifugin, and divaricatol were the main active components. Pathways in cancer and arginine and proline metabolism could be the most important pathways.

Conclusion

Our research revealed the immunoenhancing mechanisms of QSBQC and improved the combination of TCM theory and modern western medicine theory.

Precision sirolimus dosing in children: The potential for model-informed dosing and novel drug monitoring

The mTOR inhibitor sirolimus is prescribed to treat children with varying diseases, ranging from vascular anomalies to sporadic lymphangioleiomyomatosis to transplantation (solid organ or hematopoietic cell). Precision dosing of sirolimus using therapeutic drug monitoring (TDM) of sirolimus concentrations in whole blood drawn at the trough (before the next dose) time-point is the current standard of care. For sirolimus, trough concentrations are only modestly correlated with the area under the curve, with R 2 values ranging from 0.52 to 0.84. Thus, it should not be surprising, even with the use of sirolimus TDM, that patients treated with sirolimus have variable pharmacokinetics, toxicity, and effectiveness. Model-informed precision dosing (MIPD) will be beneficial and should be implemented. The data do not suggest dried blood spots point-of-care sampling of sirolimus concentrations for precision dosing of sirolimus. Future research on precision dosing of sirolimus should focus on pharmacogenomic and pharmacometabolomic tools to predict sirolimus pharmacokinetics and wearables for point-of-care quantitation and MIPD.

Status of Metabolomic Measurement for Insights in Alzheimer's Disease Progression-What Is Missing?

Alzheimer's disease (AD) is an aging-related neurodegenerative disease, leading to the progressive loss of memory and other cognitive functions. As there is still no cure for AD, the growth in the number of susceptible individuals represents a major emerging threat to public health. Currently, the pathogenesis and etiology of AD remain poorly understood, while no efficient treatments are available to slow down the degenerative effects of AD. Metabolomics allows the study of biochemical alterations in pathological processes which may be involved in AD progression and to discover new therapeutic targets. In this review, we summarized and analyzed the results from studies on metabolomics analysis performed in biological samples of AD subjects and AD animal models. Then this information was analyzed by using MetaboAnalyst to find the disturbed pathways among different sample types in human and animal models at different disease stages. We discuss the underlying biochemical mechanisms involved, and the extent to which they could impact the specific hallmarks of AD. Then we identify gaps and challenges and provide recommendations for future metabolomics approaches to better understand AD pathogenesis.

Identification of phytochemical compounds of Fagopyrum dibotrys and their targets by metabolomics, network pharmacology and molecular docking studies

Acute lung injury (ALI) is a clinically severe lung illness with high incidence rate and mortality. Especially, coronavirus disease 2019 (COVID-19) poses a serious threat to world wide governmental fitness. It has distributed to almost from corner to corner of the universe, and the situation in the prevention and control of COVID-19 remains grave. Traditional Chinese medicine plays a vital role in the precaution and therapy of sicknesses. At present, there is a lack of drugs for treating these diseases, so it is necessary to develop drugs for treating COVID-19 related ALI. Fagopyrum dibotrys (D. Don) Hara is an annual plant of the Polygonaceae family and one of the long-history used traditional medicine in China. In recent years, its rhizomes (medicinal parts) have attracted the attention of scholars at home and abroad due to their significant anti-inflammatory, antibacterial and anticancer activities. It can work on SARS-COV-2 with numerous components, targets, and pathways, and has a certain effect on coronavirus disease 2019 (COVID-19) related acute lung injury (ALI). However, there are few systematic studies on its aerial parts (including stems and leaves) and its potential therapeutic mechanism has not been studied. The phytochemical constituents of rhizome of F. dibotrys were collected using TCMSP database. And metabolites of F. dibotrys' s aerial parts were detected by metabonomics. The phytochemical targets of F. dibotrys were predicted by the PharmMapper website tool. COVID-19 and ALI-related genes were retrieved from GeneCards. Cross targets and active phytochemicals of COVID-19 and ALI related genes in F. dibotrys were enriched by gene ontology (GO) and KEGG by metscape bioinformatics tools. The interplay network entre active phytochemicals and anti COVID-19 and ALI targets was established and broke down using Cytoscape software. Discovery Studio (version 2019) was used to perform molecular docking of crux active plant chemicals with anti COVID-19 and ALI targets. We identified 1136 chemicals from the aerial parts of F. dibotrys, among which 47 were active flavonoids and phenolic chemicals. A total of 61 chemicals were searched from the rhizome of F. dibotrys, and 15 of them were active chemicals. So there are 6 commonly key active chemicals at the aerial parts and the rhizome of F. dibotrys, 89 these phytochemicals's potential targets, and 211 COVID-19 and ALI related genes. GO enrichment bespoken that F. dibotrys might be involved in influencing gene targets contained numerous biological processes, for instance, negative regulation of megakaryocyte differentiation, regulation of DNA metabolic process, which could be put down to its anti COVID-19 associated ALI effects. KEGG pathway indicated that viral carcinogenesis, spliceosome, salmonella infection, coronavirus disease - COVID-19, legionellosis and human immunodeficiency virus 1 infection pathway are the primary pathways obsessed in the anti COVID-19 associated ALI effects of F. dibotrys. Molecular docking confirmed that the 6 critical active phytochemicals of F. dibotrys, such as luteolin, (+) -epicatechin, quercetin, isorhamnetin, (+) -catechin, and (-) -catechin gallate, can combine with kernel therapeutic targets NEDD8, SRPK1, DCUN1D1, and PARP1. In vitro activity experiments showed that the total antioxidant capacity of the aerial parts and rhizomes of F. dibotrys increased with the increase of concentration in a certain range. In addition, as a whole, the antioxidant capacity of the aerial part of F. dibotrys was stronger than that of the rhizome. Our research afford cues for farther exploration of the anti COVID-19 associated ALI chemical compositions and mechanisms of F. dibotrys and afford scientific foundation for progressing modern anti COVID-19 associated ALI drugs based on phytochemicals in F. dibotrys. We also fully developed the medicinal value of F. dibotrys' s aerial parts, which can effectively avoid the waste of resources. Meanwhile, our work provides a new strategy for integrating metabonomics, network pharmacology, and molecular docking techniques which was an efficient way for recognizing effective constituents and mechanisms valid to the pharmacologic actions of traditional Chinese medicine.

A metabolomics study: Could plasma metabolites be a guide for the prevention of tamsulosin side effects?

BACKGROUND

The understanding of precision medicine, which aims for high efficacy and low toxicity in treatments, has gained more importance with omics technologies. In this study, it was aimed to reach new suggestions for low-toxicity treatment by clarifying the relationship between tamsulosin side effects and metabolome profiles.

MATERIALS AND METHODS

Plasma samples of control and tamsulosin-treated rats were analyzed by LC-Q-TOF/MS/MS. MS/MS data was processed in XCMS software for the identification of metabolite and metabolic pathway analysis. Data were classified with MATLAB 2019b for multivariate data analysis. 34m/z values were found to be significantly different between the drug and control groups (P≤0.01 and fold analysis≥1.5) and identified by comparing METLIN and HMDB databases.

RESULTS

According to multivariate data analysis, α-Linolenic Acid, Thiamine, Retinoic acid, 1.25-Dihydroxyvitamin D3-26.23-Lactone, L-Glutamine, L-Serine, Retinaldehyde, Sphingosine 1-phosphate, L-Lysine, 23S.25-Dihydroxyvitamin D3, Sphinganine, L-Cysteine, Uridine 5'-diphosphate, Calcidiol, L-Tryptophan, L-Alanine levels changed significantly compared to the control group. Differences in the metabolisms of Retinol, Sphingolipid, Alanine-Aspartate-Glutamate, Glutathione, Fatty Acid, Tryptophan, and biosynthesis of Aminoacyl-tRNA, and Unsaturated Fatty Acid have been successfully demonstrated by metabolic pathway analysis. According to our study, vitamin A and D supplements can be recommended to prevent side effects such as asthenia, rhinitis, nasal congestion, dizziness and IFIS in the treatment of tamsulosin. Alteration of aminoacyl-tRNA biosynthesis and sphingolipid metabolism pathways during tamsulosin treatment is effective in the occurrence of nasal congestion.

CONCLUSIONS

Our study provides important information for tamsulosin therapy with high efficacy and low side effects in precision medicine.

Molecular Profiling of Athletes Performing High-Intensity Exercises in Extreme Environments

The aim of this study was to determine the influence of high-intensity training under extreme conditions (T = 40 °C) on the metabolism and immunological reactions of athletes. Male triathletes (n = 11) with a high level of sports training performed load testing to failure (17 ± 2.7 min) and maximum oxygen consumption (64.1 ± 6.4 mL/min/kg). Blood plasma samples were collected before and immediately after exercise. Mass spectrometric metabolomic analysis identified 30 metabolites and 6 hormones in the plasma, of which 21 and 4 changed after exercise, respectively. Changes in the intermediate products of tricarboxylic and amino acids were observed (FC > 1.5) after exercise. The obtained data can be associated with the effect of physical activity on metabolism in athletes. Therefore, constant monitoring of the biochemical parameters of athletes can help coaches identify individual shortcomings in a timely manner and track changes, especially as the volume of training increases. In addition, it was revealed that the immunological reaction (manifestation of a hyperactive reaction to food components) is personalized in nature. Therefore, it is important for coaches and sports doctors to analyze and control the eating behavior of athletes to identify food intolerances or food allergies in a timely manner and develop an individual elimination diet.

NMR technique revealed the metabolic interference mechanism of the combined exposure to cadmium and tributyltin in grass carp larvae

Widespread human activity has resulted in the presence of different pollutants in the aquatic environment that does not exist in isolation. The study of the effects of contamination of aquatic organisms is of great significance. To assess the individual and combined toxicity of cadmium (Cd) and tributyltin (TBT) to aquatic organisms, juvenile grass carp (Ctenopharyngodon idella) were exposed to Cd (2.97 mg/L), TBT (7.5 μg/L), and their mixture MIX. The biological response was evaluated by nuclear magnetic resonance (NMR) analysis of plasma metabolites. Plasma samples at 1, 2, 4, 8, 16, 32, and 48 days post-exposure were analyzed using detection by NMR technique. The typical correlation analysis (CCA) analysis revealed that TBT had the greatest effect on plasma metabolism, followed by MIX and Cd. The interference pathway to grass carp was similar to that of TBT and MIX. Both Cd and TBT exposure alone or in combination can lead to metabolic abnormalities in TCA cycle-related pathways and interfere with energy metabolism. These results provide more detailed information for the metabolic study of pollutants and data for assessing the health risks of Cd, TBT, and MIX at the metabolic level.

UHPLC-ESI-QE-Orbitrap-MS based metabolomics reveals the antioxidant mechanism of icaritin on mice with cerebral ischemic reperfusion

Background

Icaritin (ICT) has been previously demonstrated to display protective effects against cerebral ischemic reperfusion (I/R) by inhibiting oxidative stress, but the mechanism remains unclear. This study aimed to explore the mechanism from the perspective of metabolomics.

Methods

A mice cerebral artery occlusion/reperfusion (MCAO/R) model was explored to mimic cerebral ischemic reperfusion and protective effect of ICT was assessed by neurologic deficit scoring, infarct volume and brain water content. Ultra-high-performance liquid chromatography electrospray ionization orbitrap tandem mass spectrometry (UHPLC-ESI-QE-Orbitrap-MS) based metabolomic was performed to explore potential biomarkers. Brain tissue metabolic profiles were analyzed and metabolic biomarkers were identified through multivariate data analysis. The protein levels of Nrf2, HO-1 and HQO1 were assayed by western blot. The release of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT) were detected using corresponding assay kits.

Results

The results showed that after ICT treatment, the neurological deficit, cerebral infarction area, brain edema and the level of MDA in brain tissue of MCAO/R mice were significantly reduced. Meanwhile, ICT enhanced the activity of SOD, CAT and GSH-Px. Western blot results confirmed that ICT up-regulated the protein levels of antioxidant-related protein including Nrf2, HO-1 and NQO1. According to the metabolomic profiling of brain tissues, clear separations were observed among the Sham, Model and ICT groups. A total of 44 biomarkers were identified, and the identified biomarkers were mainly related to linoleic acid metabolism, arachidonic acid metabolism, alanine, aspartate and glutamate metabolism, arginine biosynthesis, arginine and proline metabolism, D-glutamine and D-glutamate metabolism, taurine and hypotaurine metabolism and purine metabolism, respectively. At the same time, the inhibitory effect of ICT on arachidonic acid and linoleic acid in brain tissue, as well as the promoting effect on taurine, GABA, NAAG, may be the key factors for the anti-neurooxidative function of mice after MCAO/R injury.

Conclusion

Our results demonstrate that ICT has benefits for MCAO/R injury, which are partially related to the suppression of oxidative stress via stimulating the Nrf2 signaling and regulating the production of arachidonic acid, linoleic acid, taurine, GABA, NAAG in brain tissue.

20-Hydroxyecdysone and Receptor Interplay in the Regulation of Hemolymph Glucose Level in Honeybee (Apis mellifera) Larvae

The hormone 20-hydroxyecdysone (20E) and the ecdysone receptors (ECR and USP) play critical roles in the growth and metabolism of insects, including honeybees. In this study, we investigated the effect of 20E on the growth and development of honeybee larvae by rearing them in vitro and found reduced food consumption and small-sized pupae with increasing levels of 20E. A liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based analysis of widely targeted metabolomics was used to examine the changes in the metabolites after an exogenous 20E application to honeybee larvae and the underlying mechanisms. A total of 374 different metabolites were detected between the control group and the 20E treatment group, covering 12 subclasses. The most significant changes occurred in 7-day-old larvae, where some monosaccharides, such as D-Glucose and UDP-galactose, were significantly upregulated. In addition, some metabolic pathways, such as glycolysis/gluconeogenesis and galactose metabolism, were affected by the 20E treatment, suggesting that the 20E treatment disrupts the metabolic homeostasis of honeybee larvae hemolymph and that the response of honeybee larvae to the 20E treatment is dynamic and contains many complex pathways. Many genes involved in carbohydrate metabolism, including genes of the glycolysis and glycogen synthesis pathways, were downregulated during molting and pupation after the 20E treatment. In contrast, the expression levels of the genes related to gluconeogenesis and glycogenolysis were significantly increased, which directly or indirectly upregulated glucose levels in the hemolymph, whereas RNA interference with the 20E receptor EcR-USP had an opposite effect to that of the 20E treatment. Taken together, 20E plays a critical role in the changes in carbohydrate metabolism during metamorphosis.

Practical Aspects of NMR-Based Metabolomics

While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for &gt;40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5-10 years.

Analysis of metabolic differences in maize in different growth stages under nitrogen stress based on UPLC-QTOF-MS

Introduction

Maize has a high demand for nitrogen during the growth period. The study of metabolic changes in maize can provide a theoretical basis for rational nitrogen nutrition regulation.

Methods

In order to investigate the changes of different metabolites and their metabolic pathways in maize leaves under nitrogen stress, we used ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) for metabolomic analysis of maize leaves under different nitrogen treatments at three critical growth stages (V4, V12 and R1) in a pot experiment under natural conditions.

Results and discussion

The results showed that nitrogen stress significantly affected sugar metabolism and nitrogen metabolism, and affected carbon and nitrogen balance, and the effects of stress on maize leaves metabolism increased with the growth process. Metabolic pathways such as the TCA cycle and starch and sucrose metabolism were mainly affected at the seeding stage (V4). The stress response to nitrogen deficiency also showed significant upregulation of flavonoids such as luteolin and astragalin during the booting stage (V12) and anthesis-silking stage (R1). During R1 stage, the synthesis of tryptophan and phenylalanine and the degradation of lysine were significantly affected. Compared with nitrogen stress, the metabolic synthesis of key amino acids and jasmonic acid were intensified and the TCA cycle was promoted under nitrogen sufficiency conditions. This study initially revealed that the response mechanism of maize to nitrogen stress at the metabolic level.

NMR-Based Metabolomics to Evaluate Individual Response to Treatments

The aim of this chapter is to highlight the various aspects of metabolomics in relation to health and diseases, starting from the definition of metabolic space and of how individuals tend to maintain their own position in this space. Physio-pathological stimuli may cause individuals to lose their position and then regain it, or move irreversibly to other positions. By way of examples, mostly selected from our own work using ¹H NMR on biological fluids, we describe the effects on the individual metabolomic fingerprint of mild external interventions, such as diet or probiotic administration. Then we move to pathologies (such as celiac disease, various types of cancer, viral infections, and other diseases), each characterized by a well-defined metabolomic fingerprint. We describe the effects of drugs on the disease fingerprint and on its reversal to a healthy metabolomic status. Drug toxicity can be also monitored by metabolomics. We also show how the individual metabolomic fingerprint at the onset of a disease may discriminate responders from non-responders to a given drug, or how it may be prognostic of e.g., cancer recurrence after many years. In parallel with fingerprinting, profiling (i.e., the identification and quantification of many metabolites and, in the case of selected biofluids, of the lipoprotein components that contribute to the ¹H NMR spectral features) can provide hints on the metabolic pathways that are altered by a disease and assess their restoration after treatment.

EASY-FIA: A Readably Usable Standalone Tool for High-Resolution Mass Spectrometry Metabolomics Data Pre-Processing

Flow injection analysis coupled with high-resolution mass spectrometry (FIA-HRMS) is a fair trade-off between resolution and speed. However, free software available for data pre-processing is few, web-based, and often requires advanced user specialization. These tools rarely embedded blank and noise evaluation strategies, and direct feature annotation. We developed EASY-FIA, a free standalone application that can be employed for FIA-HRMS metabolomic data pre-processing by users with no bioinformatics/programming skills. We validated the tool's performance and applicability in two clinical metabolomics case studies. The main functions of our application are blank subtraction, alignment of the metabolites, and direct feature annotation by means of the Human Metabolome Database (HMDB) using a minimum number of mass spectrometry parameters. In a scenario where FIA-HRMS is increasingly recognized as a reliable strategy for fast metabolomics analysis, EASY-FIA could become a standardized and feasible tool easily usable by all scientists dealing with MS-based metabolomics. EASY-FIA was implemented in MATLAB with the App Designer tool and it is freely available for download.

Research progress on metabolomics in the quality evaluation and clinical study of Panax ginseng

Panax ginseng, an essential component of traditional medicine and often referred to as the king of herbs, has played a pivotal role in medicine globally for several millennia. Previously, traditional phytochemical methods were mainly used for quality evaluation and pharmacological mechanism studies of ginseng, resulting in the lack of systematicness and innovation and hindering the development and utilization of ginseng resources. Since the beginning of the new century, systems biology technology represented by metabolomics has shown unique advantages in the modernization and internationalization of herbal medicine, establishing a bridge for communication between traditional medicine and modern medicine. P. ginseng, a special herb used in medicine and food, is one of the main research objects for qualitative and quantitative analysis of metabolomics and has gradually become the focus of researchers globally. Here, we conducted a comprehensive summary and analysis of numerous studies published in ginseng metabolomics. This review aims to provide more novel ideas for the quality evaluation, development, and clinical application of ginseng in the future and offer more useful technical references for the modernization and internationalization of herbal medicine based on metabolomics.

Triticonazole enantiomers induced enantioselective metabolic phenotypes in Fusarium graminearum and HepG2 cells

The management of Fusarium head blight relies heavily on triazole fungicides. Most of triazole fungicides are chiral, and their enantioselective effects on metabolic phenotypes are poorly understood. Herein, we analyzed the bioactivity of triticonazole against Fusarium graminearum, and ¹H-nuclear magnetic resonance-based metabolomics was used to assess the metabolic disturbances of triticonazole enantiomers in Fusarium graminearum and human hepatocarcinoma cells. Results indicated that the bioactivity of R-triticonazole was 4.28-fold higher than its antipode since it bound stronger with fungal CYP51B and induced more abnormal metabolic processes of Fusarium graminearum, including lipid metabolism, glycolysis, and amino acid metabolism. In human hepatocarcinoma cells, pathways of "alanine, aspartic acid and glutamate metabolism" and "pyruvate metabolism" were disturbed significantly by R-triticonazole; "phenylalanine metabolism" and "taurine-hypotaurine metabolism" were abnormal in the exposure of S-triticonazole. These results suggested that R- and S-triticonazole could affect different metabolic pathways of human hepatocarcinoma cells, and the massively use of inefficient S-triticonazole should be avoided. Our data will help to better understand the enantioselectivity of chiral pesticides and provide a reference for the development of green pesticides.

Metabolomics of ischemic stroke: insights into risk prediction and mechanisms

Ischemic stroke (IS) is the most prevalent type of stroke. The early diagnosis and prognosis of IS are crucial for successful therapy and early intervention. Metabolomics, a tool in systems biology based on several innovative technologies, can be used to identify disease biomarkers and unveil underlying pathophysiological processes. Accordingly, in recent years, an increasing number of studies have identified metabolites from cerebral ischemia patients and animal models that could improve the diagnosis of IS and prediction of its outcome. In this paper, metabolomic research is comprehensively reviewed with a focus on describing the metabolic changes and related pathways associated with IS. Most clinical studies use biofluids (e.g., blood or plasma) because their collection is minimally invasive and they are ideal for analyzing changes in metabolites in patients of IS. We review the application of animal models in metabolomic analyses aimed at investigating potential mechanisms of IS and developing novel therapeutic approaches. In addition, this review presents the strengths and limitations of current metabolomic studies on IS, providing a reference for future related studies.

Alterations in the gastric microbiota and metabolites in gastric cancer: An update review

Gastric cancer (GC) is one of the leading causes of cancer mortality worldwide. Numerous studies have shown that the gastric microbiota can contribute to the occurrence and development of GC by generating harmful microbial metabolites, suggesting the possibility of discovering biomarkers. Metabolomics has emerged as an advanced promising analytical method for the analysis of microbiota-derived metabolites, which have greatly accelerated our understanding of host-microbiota metabolic interactions in GC. In this review, we briefly compiled recent research progress on the changes of gastric microbiota and its metabolites associated with GC. And we further explored the application of metabolomics and gastric microbiome association analysis in the diagnosis, prevention and treatment of GC.

Modulation of Disordered Bile Acid Homeostasis and Hepatic Tight Junctions Using Salidroside against Hepatocyte Apoptosis in Furan-Induced Mice

Furan, a processing-induced food contaminant, has attracted great attention due to its hepatotoxicity. To further investigate the underlying mechanism of salidroside (SAL) alleviating furan-induced liver damage, we divided Balb/c mice into the control group, the furan (8 mg/kg/day) group, and three groups of three different doses of SAL (10/20/40 mg/kg/day) in the current research. The shifted serum profile was observed through untargeted metabonomics, to which the bile acid metabolism was related, and the alleviating effect of SAL against furan-induced apoptosis was caused by the metabolism. Target bile acid quantification for the liver and serum showed that SAL positively regulated the homeostasis of bile acids disturbed by furan. Meanwhile, SAL significantly upregulated the synthesis genes of bile acids (Cyp7a1, Cyp7b1, Cyp8b1, and Cyp27a1) and the uptake transport genes (Ntcp and Oatps) and downregulated the efflux transport genes (Bsep, Ost-α, Ost-β, Mrp2, and Mrp4). Transmission electron microscopy of the bile canaliculi and tight junctions and the levels of tight junction marker proteins (ZO-1, occludin, and claudin-1) confirmed that the disruption of the hepatic tight junction was inhibited by SAL. The connection between the apoptosis- and tight junction-related proteins was observed through the construction of a protein-protein interaction network. SAL suppressed the furan-induced hepatocyte apoptosis evidenced by the detection of TUNEL and Bax, Bcl-2, and caspase-3 levels. Taken together, SAL alleviated furan-induced hepatocyte apoptosis via altering the disordered homeostasis of bile acids and hepatic tight junctions.