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Metabolites, Volume 10, Issue 12 (December 2020) – 42 articles

Cover Story (view full-size image): Filigree is a Java-based tool that implements our previously published Differential Network Enrichment Analysis (DNEA) algorithm. Filigree can build robust data-driven partial correlation networks from high-dimensional metabolomics and lipidomics data. If the number of metabolites far exceeds the number of samples, Filigree can perform feature aggregation to reduce data dimensionality. Our methodology can also handle imbalanced experimental designs. Filigree provides an alternative to traditional knowledge-based enrichment testing methods. We demonstrate the utility of Filigree by applying it to previously published studies analyzing the metabolome in the context of metabolic disorders. View this paper
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Article
Using Community Science to Reveal the Global Chemogeography of River Metabolomes
Metabolites 2020, 10(12), 518; https://doi.org/10.3390/metabo10120518 - 20 Dec 2020
Viewed by 1904
Abstract
River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water [...] Read more.
River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water and sediment metabolomes using ultrahigh-resolution techniques. Here, we describe a community science effort from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to characterize global metabolomes in surface water and sediment that span multiple stream orders and biomes. We describe the distribution of key aspects of metabolomes including elemental groups, chemical classes, indices, and inferred biochemical transformations. We show that metabolomes significantly differ across surface water and sediment and that surface water metabolomes are more rich and variable. We also use inferred biochemical transformations to identify core metabolic processes shared among surface water and sediment. Finally, we observe significant spatial variation in sediment metabolites between rivers in the eastern and western portions of the contiguous United States. Our work not only provides a basis for understanding global patterns in river corridor biogeochemical cycles but also demonstrates that community science endeavors can enable global research projects that are unfeasible with traditional research models. Full article
(This article belongs to the Special Issue Metabolome and Fluxomics)
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Metabolic Changes in Serum Metabolome of Beagle Dogs Fed Black Ginseng
Metabolites 2020, 10(12), 517; https://doi.org/10.3390/metabo10120517 - 19 Dec 2020
Cited by 3 | Viewed by 950
Abstract
The effects of black ginseng, which has many kinds of biological activities, on dogs was investigated. Serum samples of beagle dogs, which were fed with black ginseng for 8 weeks, were measured using high-resolution magic angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectrometry. [...] Read more.
The effects of black ginseng, which has many kinds of biological activities, on dogs was investigated. Serum samples of beagle dogs, which were fed with black ginseng for 8 weeks, were measured using high-resolution magic angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectrometry. Acquired NMR data from the serum of dogs fed for 0, 4, and 8 weeks were analyzed by metabolic profiling and multivariate statistical analysis. In statistical analysis and biomarker analysis results of metabolite profiles, formate, glutamine, histidine, isoleucine, leucine, proline, and valine had variable importance in projection (VIP) scores above 1.0 and excellent area under the curve (AUC) values of receiver operating characteristic (ROC) curves above 0.9. In the result of multivariate statistical analysis, the score plot showed the discrimination between before and after feeding of black ginseng. These differences in metabolic profiles are considered to be due to the involvement of metabolic processes following black ginseng administration, such as enhancing immunity and energy metabolism. Through metabolomics analysis, we confirmed the biological efficacy of black ginseng in dogs and also confirmed that metabolomics can be applied to the pet health industry. Full article
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Article
Exploratory Analysis of Commercial Olive-Based Dietary Supplements Using Untargeted and Targeted Metabolomics
Metabolites 2020, 10(12), 516; https://doi.org/10.3390/metabo10120516 - 19 Dec 2020
Viewed by 933
Abstract
The market of olive-based dietary supplements (OBDS) is composed of a broad range of natural extracts claiming different health effects and often sold without a clear statement on their chemical composition. The aim of this survey was to characterize the chemical profiles of [...] Read more.
The market of olive-based dietary supplements (OBDS) is composed of a broad range of natural extracts claiming different health effects and often sold without a clear statement on their chemical composition. The aim of this survey was to characterize the chemical profiles of 14 commercially available OBDS. As many as 378 compounds were tentatively annotated in the analyzed samples. Although for most of metabolites the annotation at level I was prevented due to the lack of the analytical standard, the spectra obtained from high-resolution tandem mass spectrometry (MS/MS) measurements were very informative, allowing annotation of dozens of metabolites at level II or III. A targeted method allowed the quantification of 26 selected compounds. A large qualitative and quantitative variability was observed. The products obtained from buds by glyceric maceration were those with the lowest concentrations of all the quantified elements. The dose of 5 mg of hydroxytyrosol, corresponding to the European Food Safety Authority (EFSA) health claim, was only reached by four products, all of them originating from the olive fruit or the leaves. If we also take into consideration oleuropein, two additional products provide this daily amount. This work demonstrates the high complexity and diversity in the composition of OBDS. Full article
(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics)
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Article
Evaluation of Saliva Stability for NMR Metabolomics: Collection and Handling Protocols
Metabolites 2020, 10(12), 515; https://doi.org/10.3390/metabo10120515 - 19 Dec 2020
Cited by 7 | Viewed by 968
Abstract
Maintaining a salivary metabolic profile upon sample collection and preparation is determinant in metabolomics. Nuclear magnetic resonance (NMR) spectroscopy was used to identify metabolite changes during short-term storage, at room temperature (RT)/4 °C/−20 °C, and after sample preparation, at RT/4 °C (mimicking typical [...] Read more.
Maintaining a salivary metabolic profile upon sample collection and preparation is determinant in metabolomics. Nuclear magnetic resonance (NMR) spectroscopy was used to identify metabolite changes during short-term storage, at room temperature (RT)/4 °C/−20 °C, and after sample preparation, at RT/4 °C (mimicking typical clinical/laboratory settings). Interestingly, significant metabolic inter-individual and inter-day variability were noted, probably determining sample stability to some extent. After collection, no changes were noted at −20 °C (at least for 4 weeks). RT storage induced decreases in methylated macromolecules (6 h); lactate (8 h); alanine (12 h); galactose, hypoxanthine, pyruvate (24 h); sarcosine, betaine, choline, N-acetyl-glycoproteins (48 h), while acetate increased (48 h). Less, but different, changes were observed at 4 °C, suggesting different oral and microbial status at different temperatures (with a possible contribution from inter-individual and inter-day variability), and identifying galactose, hypoxanthine, and possibly, choline esters, as potential general stability indicators. After preparation, addition of NaN3 did not impact significantly on saliva stabilization, neither at RT nor at 4 °C, although its absence was accompanied by slight increases in fucose (6.5 h) and proline (8 h) at RT, and in xylose (24 h) at 4 °C. The putative metabolic origins of the above variations are discussed, with basis on the salivary microbiome. In summary, after collection, saliva can be stored at RT/4 °C for up to 6 h and at −20 °C for at least 4 weeks. Upon preparation for NMR analysis, samples are highly stable at 25 °C up to 8 h and at 4 °C up to 48 h, with NaN3 addition preventing possible early changes in fucose, proline (6–8 h), and xylose (24 h) levels. Full article
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Article
Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma
Metabolites 2020, 10(12), 514; https://doi.org/10.3390/metabo10120514 - 18 Dec 2020
Cited by 8 | Viewed by 1512
Abstract
A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and [...] Read more.
A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91–113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis. Full article
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Article
Single-Cell Transcriptional Profiling of Mouse Islets Following Short-Term Obesogenic Dietary Intervention
Metabolites 2020, 10(12), 513; https://doi.org/10.3390/metabo10120513 - 18 Dec 2020
Cited by 4 | Viewed by 1489
Abstract
Obesity is closely associated with adipose tissue inflammation and insulin resistance. Dysglycemia and type 2 diabetes results when islet β cells fail to maintain appropriate insulin secretion in the face of insulin resistance. To clarify the early transcriptional events leading to β-cell failure [...] Read more.
Obesity is closely associated with adipose tissue inflammation and insulin resistance. Dysglycemia and type 2 diabetes results when islet β cells fail to maintain appropriate insulin secretion in the face of insulin resistance. To clarify the early transcriptional events leading to β-cell failure in the setting of obesity, we fed male C57BL/6J mice an obesogenic, high-fat diet (60% kcal from fat) or a control diet (10% kcal from fat) for one week, and islets from these mice (from four high-fat- and three control-fed mice) were subjected to single-cell RNA sequencing (sc-RNAseq) analysis. Islet endocrine cell types (α cells, β cells, δ cells, PP cells) and other resident cell types (macrophages, T cells) were annotated by transcript profiles and visualized using Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) plots. UMAP analysis revealed distinct cell clusters (11 for β cells, 5 for α cells, 3 for δ cells, PP cells, ductal cells, endothelial cells), emphasizing the heterogeneity of cell populations in the islet. Collectively, the clusters containing the majority of β cells showed the fewest gene expression changes, whereas clusters harboring the minority of β cells showed the most changes. We identified that distinct β-cell clusters downregulate genes associated with the endoplasmic reticulum stress response and upregulate genes associated with insulin secretion, whereas others upregulate genes that impair insulin secretion, cell proliferation, and cell survival. Moreover, all β-cell clusters negatively regulate genes associated with immune response activation. Glucagon-producing α cells exhibited patterns similar to β cells but, again, in clusters containing the minority of α cells. Our data indicate that an early transcriptional response in islets to an obesogenic diet reflects an attempt by distinct populations of β cells to augment or impair cellular function and/or reduce inflammatory responses as possible harbingers of ensuing insulin resistance. Full article
(This article belongs to the Special Issue Islet Inflammation and Metabolic Homeostasis)
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Review
Fatty Acyl Esters of Hydroxy Fatty Acid (FAHFA) Lipid Families
Metabolites 2020, 10(12), 512; https://doi.org/10.3390/metabo10120512 - 17 Dec 2020
Cited by 4 | Viewed by 1050
Abstract
Fatty Acyl esters of Hydroxy Fatty Acids (FAHFA) encompass three different lipid families which have incorrectly been classified as wax esters. These families include (i) Branched-chain FAHFAs, involved in the regulation of glucose metabolism and inflammation, with acylation of an internal branched-chain hydroxy-palmitic [...] Read more.
Fatty Acyl esters of Hydroxy Fatty Acids (FAHFA) encompass three different lipid families which have incorrectly been classified as wax esters. These families include (i) Branched-chain FAHFAs, involved in the regulation of glucose metabolism and inflammation, with acylation of an internal branched-chain hydroxy-palmitic or -stearic acid; (ii) ω-FAHFAs, which function as biosurfactants in a number of biofluids, are formed via acylation of the ω-hydroxyl group of very-long-chain fatty acids (these lipids have also been designated as o-acyl hydroxy fatty acids; OAHFA); and (iii) Ornithine-FAHFAs are bacterial lipids formed by the acylation of short-chain 3-hydroxy fatty acids and the addition of ornithine to the free carboxy group of the hydroxy fatty acid. The differences in biosynthetic pathways and cellular functions of these lipid families will be reviewed and compared to wax esters, which are formed by the acylation of a fatty alcohol, not a hydroxy fatty acid. In summary, FAHFA lipid families are both unique and complex in their biosynthesis and their biological actions. We have only evaluated the tip of the iceberg and much more exciting research is required to understand these lipids in health and disease. Full article
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Review
The Metabolomics of Childhood Atopic Diseases: A Comprehensive Pathway-Specific Review
Metabolites 2020, 10(12), 511; https://doi.org/10.3390/metabo10120511 - 16 Dec 2020
Cited by 6 | Viewed by 1114
Abstract
Asthma, allergic rhinitis, food allergy, and atopic dermatitis are common childhood diseases with several different underlying mechanisms, i.e., endotypes of disease. Metabolomics has the potential to identify disease endotypes, which could beneficially promote personalized prevention and treatment. Here, we summarize the findings from [...] Read more.
Asthma, allergic rhinitis, food allergy, and atopic dermatitis are common childhood diseases with several different underlying mechanisms, i.e., endotypes of disease. Metabolomics has the potential to identify disease endotypes, which could beneficially promote personalized prevention and treatment. Here, we summarize the findings from metabolomics studies of children with atopic diseases focusing on tyrosine and tryptophan metabolism, lipids (particularly, sphingolipids), polyunsaturated fatty acids, microbially derived metabolites (particularly, short-chain fatty acids), and bile acids. We included 25 studies: 23 examined asthma or wheezing, five examined allergy endpoints, and two focused on atopic dermatitis. Of the 25 studies, 20 reported findings in the pathways of interest with findings for asthma in all pathways and for allergy and atopic dermatitis in most pathways except tyrosine metabolism and short-chain fatty acids, respectively. Particularly, tyrosine, 3-hydroxyphenylacetic acid, N-acetyltyrosine, tryptophan, indolelactic acid, 5-hydroxyindoleacetic acid, p-Cresol sulfate, taurocholic acid, taurochenodeoxycholic acid, glycohyocholic acid, glycocholic acid, and docosapentaenoate n-6 were identified in at least two studies. This pathway-specific review provides a comprehensive overview of the existing evidence from metabolomics studies of childhood atopic diseases. The altered metabolic pathways uncover some of the underlying biochemical mechanisms leading to these common childhood disorders, which may become of potential value in clinical practice. Full article
(This article belongs to the Special Issue Metabolomics and Its Application in Human Diseases Volume 2)
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Article
Possible Influence of Weight Gain and Creatinine Levels in Predicting Response to Nivolumab: A Multicenter Analysis
Metabolites 2020, 10(12), 510; https://doi.org/10.3390/metabo10120510 - 14 Dec 2020
Viewed by 981
Abstract
Literature suggests that high body mass index can be correlated with better response to immune checkpoint inhibitors. On the other hand, sarcopenia seems to be a negative predictive marker. The present analysis is a retrospective, multicenter trial that included patients with metastatic melanoma, [...] Read more.
Literature suggests that high body mass index can be correlated with better response to immune checkpoint inhibitors. On the other hand, sarcopenia seems to be a negative predictive marker. The present analysis is a retrospective, multicenter trial that included patients with metastatic melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma treated with nivolumab between 2018 and 2020. Patients were stratified by creatinine levels both at treatment initiation and at first follow-up (at three months) and by BMI for the same intervals, as recorded in the patients’ charts. Creatinine was considered a surrogate marker for sarcopenia. IBM SPSS version 20 was used for statistical analysis. A total of 57 (n = 57) patients were included in the trial. Overall response rate (ORR) for the entire population was 38.59% (p = 0.02). Patients with BMI lower than 25 had an ORR of 28.5% (p = 0.003), whereas patients with BMI higher than 25 had an ORR of 42.3% (p = 0.002). Patients who gained weight during treatment had a lower probability of having progressive disease (OR = 0.4 [95% CI; 0.4–1.2]), as did patients with creatinine higher than 0.9 (OR = 0.39 [95% CI: 0.13–1.14]). No superiority was found in progression-free survival (PFS) when patients were dichotomized for BMI = 25 or BMI = 18.5. Mean PFS in the BMI under 18.5 group was 10.2 months [95% CI: 5.8–23.1], versus 11.2 for BMI over 18.5 [95% CI: 5.3–25.3], p < 0.03. Mean PFS for the BMI under 25 was 11.2 months [95% CI: 7.2–20.1], vs. 13.3 months [95% CI: 6.4–22] for the BMI over 25, p < 0.001. There were also differences in PFS in the patients with baseline creatinine over 0.9 when compared with under 0.9 values. Mean PFS in the first group was 19.78 months [95% CI: 16.23–22.9] vs. 16.1 [95% CI: 12.2–20.3], p < 0.001. Patients treated with nivolumab who have weight gain during treatment have a better PFS than the ones who do not. Creatinine levels of over 0.9 at treatment initiation also have positive predictive value. Full article
(This article belongs to the Special Issue Cardiometabolic Challenges-Present and Future)
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Article
Integration of Lipidomics and Transcriptomics Reveals Reprogramming of the Lipid Metabolism and Composition in Clear Cell Renal Cell Carcinoma
Metabolites 2020, 10(12), 509; https://doi.org/10.3390/metabo10120509 - 13 Dec 2020
Cited by 11 | Viewed by 1385
Abstract
Clear cell renal cell carcinoma (ccRCC) is fundamentally a metabolic disease. Given the importance of lipids in many cellular processes, in this study we delineated a lipidomic profile of human ccRCC and integrated it with transcriptomic data to connect the variations in cancer [...] Read more.
Clear cell renal cell carcinoma (ccRCC) is fundamentally a metabolic disease. Given the importance of lipids in many cellular processes, in this study we delineated a lipidomic profile of human ccRCC and integrated it with transcriptomic data to connect the variations in cancer lipid metabolism with gene expression changes. Untargeted lipidomic analysis was performed on 20 ccRCC and 20 paired normal tissues, using LC-MS and GC-MS. Different lipid classes were altered in cancer compared to normal tissue. Among the long chain fatty acids (LCFAs), significant accumulations of polyunsaturated fatty acids (PUFAs) were found. Integrated lipidomic and transcriptomic analysis showed that fatty acid desaturation and elongation pathways were enriched in neoplastic tissue. Consistent with these findings, we observed increased expression of stearoyl-CoA desaturase (SCD1) and FA elongase 2 and 5 in ccRCC. Primary renal cancer cells treated with a small molecule SCD1 inhibitor (A939572) proliferated at a slower rate than untreated cancer cells. In addition, after cisplatin treatment, the death rate of tumor cells treated with A939572 was significantly greater than that of untreated cancer cells. In conclusion, our findings delineate a ccRCC lipidomic signature and showed that SCD1 inhibition significantly reduced cancer cell proliferation and increased cisplatin sensitivity, suggesting that this pathway can be involved in ccRCC chemotherapy resistance. Full article
(This article belongs to the Special Issue Metabolomics in Kidney Disease)
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Article
A New Approach for the Production of Selenium-Enriched and Probiotic Yeast Biomass from Agro-Industrial by-Products in a Stirred-Tank Bioreactor
Metabolites 2020, 10(12), 508; https://doi.org/10.3390/metabo10120508 - 13 Dec 2020
Viewed by 901
Abstract
The production of biomolecules using agro-industrial by-products as feedstock is a growing trend worldwide. Selenium (Se) is a trace element essential for health, and the Se-enrichment of yeast biomass can enhance its benefits. This study investigated the feasibility of the production of Saccharomyces [...] Read more.
The production of biomolecules using agro-industrial by-products as feedstock is a growing trend worldwide. Selenium (Se) is a trace element essential for health, and the Se-enrichment of yeast biomass can enhance its benefits. This study investigated the feasibility of the production of Saccharomyces cerevisiae Se-enriched biomass using a medium composed of corn bran and soybean bran acid hydrolysates as carbon and nitrogen sources in a stirred-tank reactor. After hydrolysis, hydrolysates presented complex composition and high concentrations of sugars, proteins, and minerals. The use of a stirred-tank bioreactor leads to the production of 9 g/L S. cerevisiae biomass enriched with 236.93 μg/g Se, and 99% cell viability. Likewise, the combination of sugarcane molasses and soybean bran hydrolysate was effective for cell growth of a probiotic strain of S. cerevisiae with a 24.08% β-glucan content. The results demonstrated that starchy acid hydrolysates are low-cost and efficient substrates for the production of yeast biomass and derivate products and may contribute to further studies for a sustainable development of biorefinery technologies. Full article
(This article belongs to the Special Issue Metabolites Produced by Yeast Cells)
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Article
Comparative Analysis of Milk Triglycerides Profile between Jaffarabadi Buffalo and Holstein Friesian Cow
Metabolites 2020, 10(12), 507; https://doi.org/10.3390/metabo10120507 - 11 Dec 2020
Viewed by 1022
Abstract
Milk lipids are known for a variety of biological functions, however; little is known about compositional variation across breeds, especially for Jaffarabadi buffalo, an indigenous Indian breed. Systematic profiling of extracted milk lipids was performed by mass spectrometry across summer and winter in [...] Read more.
Milk lipids are known for a variety of biological functions, however; little is known about compositional variation across breeds, especially for Jaffarabadi buffalo, an indigenous Indian breed. Systematic profiling of extracted milk lipids was performed by mass spectrometry across summer and winter in Holstein Friesian cow and Jaffarabadi buffalo. Extensive MS/MS spectral analysis for the identification (ID) of probable lipid species using software followed by manual verification and grading of each assigned lipid species enabled ID based on (a) parent ion, (b) head group, and (c) partial/full acyl characteristic ions for comparative profiling of triacylglycerols between the breeds. Additionally, new triacylglycerol species with short-chain fatty acids were reported by manual interpretation of MS/MS spectra and comparison with curated repositories. Collectively, 1093 triacylglycerol species belonging to 141 unique sum compositions between the replicates of both the animal groups were identified. Relative quantitation at sum composition level followed by statistical analyses revealed changes in relative abundances of triacylglycerol species due to breed, season, and interaction effect of the two. Significant changes in triacylglycerols were observed between breeds (81%) and seasons (59%). When the interaction effect is statistically significant, a higher number of triacylglycerols species in Jaffarabadi has lesser seasonal variation than Holstein Friesian. Full article
(This article belongs to the Special Issue Nutritional Metabolomics)
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Article
Using an Untargeted Metabolomics Approach to Identify Salivary Metabolites in Women with Breast Cancer
Metabolites 2020, 10(12), 506; https://doi.org/10.3390/metabo10120506 - 10 Dec 2020
Cited by 3 | Viewed by 877
Abstract
Metabolic alterations are a hallmark of the malignant transformation in cancer cells, which is characterized by multiple changes in metabolic pathways that are linked to macromolecule synthesis. This study aimed to explore whether salivary metabolites could help discriminate between breast cancer patients and [...] Read more.
Metabolic alterations are a hallmark of the malignant transformation in cancer cells, which is characterized by multiple changes in metabolic pathways that are linked to macromolecule synthesis. This study aimed to explore whether salivary metabolites could help discriminate between breast cancer patients and healthy controls. Saliva samples from 23 breast cancer patients and 35 healthy controls were subjected to untargeted metabolomics using liquid chromatography-quadrupole time-of-flight mass spectrometry and a bioinformatics tool (XCMS Online), which revealed 534 compounds, characterized by their retention time in reverse-phase liquid chromatography and by the m/z ratio detected, that were shared by the two groups. Using the METLIN database, 31 compounds that were upregulated in the breast cancer group (p < 0.05) were identified, including seven oligopeptides and six glycerophospholipids (PG14:2, PA32:1, PS28:0, PS40:6, PI31:1, and PI38:7). In addition, pre-treatment and post-treatment saliva samples were analyzed for 10 patients who experienced at least a partial response to their treatment. In these patients, three peptides and PG14:2 were upregulated before but not after treatment. The area under the curve, sensitivity, and specificity for PG14:2 was 0.7329, 65.22%, and 77.14%, respectively. These results provide new information regarding the salivary metabolite profiles of breast cancer patients, which may be useful biomarkers. Full article
(This article belongs to the Section Endocrinology and Clinical Metabolic Research)
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Review
Biostimulants for Plant Growth and Mitigation of Abiotic Stresses: A Metabolomics Perspective
Metabolites 2020, 10(12), 505; https://doi.org/10.3390/metabo10120505 - 10 Dec 2020
Cited by 15 | Viewed by 2247
Abstract
Adverse environmental conditions due to climate change, combined with declining soil fertility, threaten food security. Modern agriculture is facing a pressing situation where novel strategies must be developed for sustainable food production and security. Biostimulants, conceptually defined as non-nutrient substances or microorganisms with [...] Read more.
Adverse environmental conditions due to climate change, combined with declining soil fertility, threaten food security. Modern agriculture is facing a pressing situation where novel strategies must be developed for sustainable food production and security. Biostimulants, conceptually defined as non-nutrient substances or microorganisms with the ability to promote plant growth and health, represent the potential to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and crop productivity. Current knowledge and phenotypic observations suggest that biostimulants potentially function in regulating and modifying physiological processes in plants to promote growth, alleviate stresses, and improve quality and yield. However, to successfully develop novel biostimulant-based formulations and programs, understanding biostimulant-plant interactions, at molecular, cellular and physiological levels, is a prerequisite. Metabolomics, a multidisciplinary omics science, offers unique opportunities to predictively decode the mode of action of biostimulants on crop plants, and identify signatory markers of biostimulant action. Thus, this review intends to highlight the current scientific efforts and knowledge gaps in biostimulant research and industry, in context of plant growth promotion and stress responses. The review firstly revisits models that have been elucidated to describe the molecular machinery employed by plants in coping with environmental stresses. Furthermore, current definitions, claims and applications of plant biostimulants are pointed out, also indicating the lack of biological basis to accurately postulate the mechanisms of action of plant biostimulants. The review articulates briefly key aspects in the metabolomics workflow and the (potential) applications of this multidisciplinary omics science in the biostimulant industry. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
The Ketogenic Diet Increases In Vivo Glutathione Levels in Patients with Epilepsy
Metabolites 2020, 10(12), 504; https://doi.org/10.3390/metabo10120504 - 10 Dec 2020
Cited by 3 | Viewed by 935
Abstract
The Ketogenic Diet (KD) is a high-fat, low-carbohydrate diet that has been utilized as the first line treatment for contrasting intractable epilepsy. It is responsible for the presence of ketone bodies in blood, whose neuroprotective effect has been widely shown in recent years [...] Read more.
The Ketogenic Diet (KD) is a high-fat, low-carbohydrate diet that has been utilized as the first line treatment for contrasting intractable epilepsy. It is responsible for the presence of ketone bodies in blood, whose neuroprotective effect has been widely shown in recent years but remains unclear. Since glutathione (GSH) is implicated in oxidation-reduction reactions, our aim was to monitor the effects of KD on GSH brain levels by means of magnetic resonance spectroscopy (MRS). MRS was acquired from 16 KD patients and seven age-matched Healthy Controls (HC). We estimated metabolite concentrations with linear combination model (LCModel), assessing differences between KD and HC with t-test. Pearson was used to investigate GHS correlations with blood serum 3-B-Hydroxybutyrate (3HB) concentrations and with number of weekly epileptic seizures. The results have shown higher levels of brain GSH for KD patients (2.5 ± 0.5 mM) compared to HC (2.0 ± 0.5 mM). Both blood serum 3HB and number of seizures did not correlate with GSH concentration. The present study showed a significant increase in GSH in the brain of epileptic children treated with KD, reproducing for the first time in humans what was previously observed in animal studies. Our results may suggest a pivotal role of GSH in the antioxidant neuroprotective effect of KD in the human brain. Full article
(This article belongs to the Section Frontiers in Metabolomics)
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Article
Effects of Dietary Defatted Meat Species on Metabolomic Profiles of Murine Liver, Gastrocnemius Muscle, and Cecal Content
Metabolites 2020, 10(12), 503; https://doi.org/10.3390/metabo10120503 - 09 Dec 2020
Viewed by 1171
Abstract
In both humans and animals, meat not only constitutes one of the sources of protein, but also includes various water-soluble bioactive substances such as imidazole peptides (carnosine and anserine) and taurine. Previous studies demonstrated that dietary meat species could differently affect physiological functions; [...] Read more.
In both humans and animals, meat not only constitutes one of the sources of protein, but also includes various water-soluble bioactive substances such as imidazole peptides (carnosine and anserine) and taurine. Previous studies demonstrated that dietary meat species could differently affect physiological functions; however, the mechanisms of this remain unclear. To explore the physiological effects of dietary defatted meat species, especially on metabolism, we investigated their influence on the metabolomic profiles of the liver, gastrocnemius muscle, and cecal content in mice. Casein (control) or a defatted meat species (beef leg, pork leg, chicken leg, or chicken breast) was supplied as the major protein source in the diet for four weeks, and metabolism-related molecules were measured by gas chromatography–mass spectrometry. We found that various metabolite levels in tissues and cecal content differed according to the types of dietary protein consumed. Specifically, differences in carnosine, 1,5-anhydro-glucitol, inositol, butyric acid, and propionic acid were clearly observed. Among them, the highest carnosine intake by dietary pork leg was clearly related to the highest carnosine level in the liver. In addition, taurine intake was suggested to be linked to some metabolic pathways including taurine and hypotaurine metabolism in cecal content. These results provide additional knowledge of the effects of different dietary meat species on human and animal health. Full article
(This article belongs to the Special Issue Metabolomic Applications in Animal Science Volume 2)
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Article
Prediction of Autoimmune Diseases by Targeted Metabolomic Assay of Urinary Organic Acids
Metabolites 2020, 10(12), 502; https://doi.org/10.3390/metabo10120502 - 08 Dec 2020
Cited by 6 | Viewed by 4013
Abstract
Autoimmune diseases (ADs) are chronic disorders characterized by the loss of self-tolerance, and although being heterogeneous, they share common pathogenic mechanisms. Self-antigens and inflammation markers are established diagnostic tools; however, the metabolic imbalances that underlie ADs are poorly described. The study aimed to [...] Read more.
Autoimmune diseases (ADs) are chronic disorders characterized by the loss of self-tolerance, and although being heterogeneous, they share common pathogenic mechanisms. Self-antigens and inflammation markers are established diagnostic tools; however, the metabolic imbalances that underlie ADs are poorly described. The study aimed to employ metabolomics for the detection of disease-related changes in autoimmune diseases that could have predictive value. Quantitative analysis of 28 urine organic acids was performed using Gas Chromatography-Mass Spectrometry in a group of 392 participants. Autoimmune thyroiditis, inflammatory bowel disease, psoriasis and rheumatoid arthritis were the most prevalent autoimmune diseases of the study. Statistically significant differences were observed in the tricarboxylate cycle metabolites, succinate, methylcitrate and malate, the pyroglutamate and 2-hydroxybutyrate from the glutathione cycle and the metabolites methylmalonate, 4-hydroxyphenylpyruvate, 2-hydroxyglutarate and 2-hydroxyisobutyrate between the AD group and the control. Artificial neural networks and Binary logistic regression resulted in the highest predictive accuracy scores (66.7% and 74.9%, respectively), while Methylmalonate, 2-Hydroxyglutarate and 2-hydroxybutyrate were proposed as potential biomarkers for autoimmune diseases. Urine organic acid levels related to the mechanisms of energy production and detoxification were associated with the presence of autoimmune diseases and could be an adjunct tool for early diagnosis and prediction. Full article
(This article belongs to the Special Issue Metabolomics and Its Application in Human Diseases Volume 2)
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Article
Oral Gavage Delivery of Stable Isotope Tracer for In Vivo Metabolomics
Metabolites 2020, 10(12), 501; https://doi.org/10.3390/metabo10120501 - 08 Dec 2020
Cited by 5 | Viewed by 1564
Abstract
Stable isotope-resolved metabolomics (SIRM) is a powerful tool for understanding disease. Advances in SIRM techniques have improved isotopic delivery and expanded the workflow from exclusively in vitro applications to in vivo methodologies to study systemic metabolism. Here, we report a simple, minimally-invasive and [...] Read more.
Stable isotope-resolved metabolomics (SIRM) is a powerful tool for understanding disease. Advances in SIRM techniques have improved isotopic delivery and expanded the workflow from exclusively in vitro applications to in vivo methodologies to study systemic metabolism. Here, we report a simple, minimally-invasive and cost-effective method of tracer delivery to study SIRM in vivo in laboratory mice. Following a brief fasting period, we orally administered a solution of [U-13C] glucose through a blunt gavage needle without anesthesia, at a physiological dose commonly used for glucose tolerance tests (2 g/kg bodyweight). We defined isotopic enrichment in plasma and tissue at 15, 30, 120, and 240 min post-gavage. 13C-labeled glucose peaked in plasma around 15 min post-gavage, followed by period of metabolic decay and clearance until 4 h. We demonstrate robust enrichment of a variety of central carbon metabolites in the plasma, brain and liver of C57/BL6 mice, including amino acids, neurotransmitters, and glycolytic and tricarboxylic acid (TCA) cycle intermediates. We then applied this method to study in vivo metabolism in two distinct mouse models of diseases known to involve dysregulation of glucose metabolism: Alzheimer’s disease and type II diabetes. By delivering [U-13C] glucose via oral gavage to the 5XFAD Alzheimer’s disease model and the Lepob/ob type II diabetes model, we were able to resolve significant differences in multiple central carbon pathways in both model systems, thus providing evidence of the utility of this method to study diseases with metabolic components. Together, these data clearly demonstrate the efficacy and efficiency of an oral gavage delivery method, and present a clear time course for 13C enrichment in plasma, liver and brain of mice following oral gavage of [U-13C] glucose—data we hope will aid other researchers in their own 13C-glucose metabolomics study design. Full article
(This article belongs to the Special Issue Stable Isotope Guided Metabolomics)
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Article
Caulerpa lentillifera (Sea Grapes) Improves Cardiovascular and Metabolic Health of Rats with Diet-Induced Metabolic Syndrome
Metabolites 2020, 10(12), 500; https://doi.org/10.3390/metabo10120500 - 07 Dec 2020
Cited by 4 | Viewed by 1662
Abstract
Caulerpa lentillifera (sea grapes) is widely consumed in South-East Asia as a low-energy food with high contents of vitamins and minerals. This study investigated dried sea grapes containing 16.6% insoluble fibre commercially produced in Vietnam as an intervention. We hypothesised that insoluble fibre [...] Read more.
Caulerpa lentillifera (sea grapes) is widely consumed in South-East Asia as a low-energy food with high contents of vitamins and minerals. This study investigated dried sea grapes containing 16.6% insoluble fibre commercially produced in Vietnam as an intervention. We hypothesised that insoluble fibre is the primary metabolite that will reverse diet-induced metabolic syndrome. Male Wistar rats (n = 48) were randomly allocated to four groups in a 16 week protocol. Two groups were fed either corn starch (C) or high-carbohydrate, high-fat (H) diets for the full 16 weeks. The other two groups received C and H diets for eight weeks and then received C. lentillifera added to these diets for the final eight weeks (CCL and HCL, respectively). High-carbohydrate, high-fat diet-fed rats developed obesity, hypertension, dyslipidaemia, fatty liver disease and increased left ventricular collagen deposition. C. lentillifera supplementation in HCL rats decreased body weight, systolic blood pressure, plasma concentrations of total cholesterol and non-esterified fatty acids, inflammatory cells in heart and liver, and visceral adiposity. The Firmicutes to Bacteroidetes ratio decreased in the gut microbiota of HCL rats. Therefore, C. lentillifera attenuated cardiovascular and metabolic symptoms of metabolic syndrome in rats, possibly by preventing infiltration of inflammatory cells together with modulating gut microbiota. Full article
(This article belongs to the Special Issue Seaweeds Metabolites Volume 2)
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Review
Vitamin D Metabolism and Its Role in Mineral and Bone Disorders in Chronic Kidney Disease in Humans, Dogs and Cats
Metabolites 2020, 10(12), 499; https://doi.org/10.3390/metabo10120499 - 04 Dec 2020
Cited by 1 | Viewed by 885
Abstract
Some differences regarding Vitamin D metabolism are described in dogs and cats in comparison with humans, which may be explained by an evolutionary drive among these species. Similarly, vitamin D is one of the most important regulators of mineral metabolism in dogs and [...] Read more.
Some differences regarding Vitamin D metabolism are described in dogs and cats in comparison with humans, which may be explained by an evolutionary drive among these species. Similarly, vitamin D is one of the most important regulators of mineral metabolism in dogs and cats, as well as in humans. Mineral metabolism is intrinsically related to bone metabolism, thus disturbances in vitamin D have been implicated in the development of chronic kidney disease mineral and bone disorders (CKD-MBD) in people, in addition to dogs and cats. Vitamin D deficiency may be associated with Renal Secondary Hyperparathyroidism (RSHPT), which is the most common mineral disorder in later stages of CKD in dogs and cats. Herein, we review the peculiarities of vitamin D metabolism in these species in comparison with humans, and the role of vitamin D disturbances in the development of CKD-MBD among dogs, cats, and people. Comparative studies may offer some evidence to help further research about vitamin D metabolism and bone disorders in CKD. Full article
(This article belongs to the Special Issue Vitamin D and Bone Metabolism)
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Article
Metabolic Signatures of Gestational Weight Gain and Postpartum Weight Loss in a Lifestyle Intervention Study of Overweight and Obese Women
Metabolites 2020, 10(12), 498; https://doi.org/10.3390/metabo10120498 - 04 Dec 2020
Viewed by 1275
Abstract
Background: Overweight and obesity amongst women of reproductive age are increasingly common in developed economies and are shown to adversely affect birth outcomes and both childhood and adulthood health risks in the offspring. Metabolic profiling in conditions of overweight and obesity in pregnancy [...] Read more.
Background: Overweight and obesity amongst women of reproductive age are increasingly common in developed economies and are shown to adversely affect birth outcomes and both childhood and adulthood health risks in the offspring. Metabolic profiling in conditions of overweight and obesity in pregnancy could potentially be applied to elucidate the molecular basis of the adverse effects of gestational weight gain (GWG) and postpartum weight loss (WL) on future risks for cardiovascular disease (CVD) and other chronic diseases. Methods: Biofluid samples were collected from 114 ethnically diverse pregnant women with body mass index (BMI) between 25 and 40 kg/m2 from Chicago (US), as part of a randomized lifestyle intervention trial (Maternal Offspring Metabolics: Family Intervention Trial; NCT01631747). At 15 weeks, 35 weeks of gestation, and at 1 year postpartum, the blood plasma lipidome and metabolic profile of urine samples were analyzed by liquid chromatography mass spectrometry (LC-MS) and 1H nuclear magnetic resonance spectroscopy (1H NMR) respectively. Results: Urinary 4-deoxyerythronic acid and 4-deoxythreonic acid were found to be positively correlated to BMI. Seventeen plasma lipids were found to be associated with GWG and 16 lipids were found to be associated with WL, which included phosphatidylinositols (PI), phosphatidylcholines (PC), lysophospholipids (lyso-), sphingomyelins (SM) and ether phosphatidylcholine (PC-O). Three phospholipids found to be positively associated with GWG all contained palmitate side-chains, and amongst the 14 lipids that were negatively associated with GWG, seven were PC-O. Six of eight lipids found to be negatively associated with WL contained an 18:2 fatty acid side-chain. Conclusions: Maternal obesity was associated with characteristic urine and plasma metabolic phenotypes, and phospholipid profile was found to be associated with both GWG and postpartum WL in metabolically healthy pregnant women with overweight/obesity. Postpartum WL may be linked to the reduction in the intake of linoleic acid/conjugated linoleic acid food sources in our study population. Full article
(This article belongs to the Special Issue Nutrients and Metabolic Syndrome)
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Article
Phytochemical Profile and Antioxidant Activity of Aerial and Underground Parts of Salvia bulleyana Diels. Plants
Metabolites 2020, 10(12), 497; https://doi.org/10.3390/metabo10120497 - 03 Dec 2020
Cited by 6 | Viewed by 881
Abstract
Plants have been used for medical purposes since ancient times. However, a detailed analysis of their biological properties and their associated active compounds is needed to justify their therapeutic use in modern medicine. The aim of the study was to identify and quantify [...] Read more.
Plants have been used for medical purposes since ancient times. However, a detailed analysis of their biological properties and their associated active compounds is needed to justify their therapeutic use in modern medicine. The aim of the study was to identify and quantify the phenolics present in hydromethanolic extracts of the roots and shoots of the Chinese Salvia species, Salvia bulleyana. The qualitative and quantitative analyses were carried out by ultrahigh-performance liquid chromatography with electrospray ionization mass spectrometry detection (UHPLC-PDA-ESI-MS), and high-performance liquid chromatography with photodiode array (HPLC-PDA) detection. The extracts of S. bulleyana were also screened for their antioxidant activity using ferric ion (Fe3+) reducing antioxidant power (FRAP), 1,1-diphenyl-2-picrylhydrazyl (DPPH), diammonium 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) cation (ABTS), superoxide radical anion (O2•–), and inhibition of lipid peroxidation assays. The S. bulleyana extracts were found to contain 38 substances, of which 36 were phenols, with a total level of 14.4 mg/g DW (dry weight) in shoots, and 23.1 mg/g DW in roots. Twenty-eight phenols were polyphenolic acids or their derivatives, the most abundant in shoots being rosmarinic acid, and in roots, salvianolic acid K followed by rosmarinic acid. The other major phenolic acids were caffeic acid, caffeoyl-threonic acids, isomers of lithospermic acid, salvianolic acid F, salvianolic acid B, and yunnaneic acid E. In addition to polyphenolic acids, nine flavonoids were detected in the shoot extract. While both extracts showed significant antioxidant activity, the shoot extract, containing both polyphenolic acids and flavonoids, demonstrated a slightly greater antioxidant potential in some of the anti-radical tests than the roots. However, the root extract proved to be slightly more effective in the lipid peroxidation inhibition test. Thus, S. bulleyana was demonstrated as a promising source of antioxidants, and worthy of further more detailed studies. Full article
(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics)
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Review
The Role of Vitamin D in Small Animal Bone Metabolism
Metabolites 2020, 10(12), 496; https://doi.org/10.3390/metabo10120496 - 03 Dec 2020
Cited by 4 | Viewed by 893
Abstract
Dogs and cats have differences in vitamin D metabolism compared to other mammalian species, as they are unable to perform vitamin D cutaneous synthesis through sun exposure. Therefore, they are dependent on the dietary intake of this nutrient. The classic functions of vitamin [...] Read more.
Dogs and cats have differences in vitamin D metabolism compared to other mammalian species, as they are unable to perform vitamin D cutaneous synthesis through sun exposure. Therefore, they are dependent on the dietary intake of this nutrient. The classic functions of vitamin D are to stimulate intestinal calcium and phosphate absorption, renal calcium and phosphate reabsorption and regulate bone mineral metabolism. Thus, it is an important nutrient for calcium and phosphorus homeostasis. This review highlights the evidence of the direct and indirect actions of vitamin D on bone mineral metabolism, the consequences of nutritional imbalances of this nutrient in small animals, as well as differences in vitamin D metabolism between different size dogs. Full article
(This article belongs to the Special Issue Vitamin D and Bone Metabolism)
Article
Single-Step Extraction Coupled with Targeted HILIC-MS/MS Approach for Comprehensive Analysis of Human Plasma Lipidome and Polar Metabolome
Metabolites 2020, 10(12), 495; https://doi.org/10.3390/metabo10120495 - 02 Dec 2020
Cited by 3 | Viewed by 2744
Abstract
Expanding metabolome coverage to include complex lipids and polar metabolites is essential in the generation of well-founded hypotheses in biological assays. Traditionally, lipid extraction is performed by liquid-liquid extraction using either methyl-tert-butyl ether (MTBE) or chloroform, and polar metabolite extraction using methanol. Here, [...] Read more.
Expanding metabolome coverage to include complex lipids and polar metabolites is essential in the generation of well-founded hypotheses in biological assays. Traditionally, lipid extraction is performed by liquid-liquid extraction using either methyl-tert-butyl ether (MTBE) or chloroform, and polar metabolite extraction using methanol. Here, we evaluated the performance of single-step sample preparation methods for simultaneous extraction of the complex lipidome and polar metabolome from human plasma. The method performance was evaluated using high-coverage Hydrophilic Interaction Liquid Chromatography-ESI coupled to tandem mass spectrometry (HILIC-ESI-MS/MS) methodology targeting a panel of 1159 lipids and 374 polar metabolites. The criteria used for method evaluation comprised protein precipitation efficiency, and relative MS signal abundance and repeatability of detectable lipid and polar metabolites in human plasma. Among the tested methods, the isopropanol (IPA) and 1-butanol:methanol (BUME) mixtures were selected as the best compromises for the simultaneous extraction of complex lipids and polar metabolites, allowing for the detection of 584 lipid species and 116 polar metabolites. The extraction with IPA showed the greatest reproducibility with the highest number of lipid species detected with the coefficient of variation (CV) < 30%. Besides this difference, both IPA and BUME allowed for the high-throughput extraction and reproducible measurement of a large panel of complex lipids and polar metabolites, thus warranting their application in large-scale human population studies. Full article
(This article belongs to the Special Issue Sample Preparation in Metabolomics)
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Article
Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS
Metabolites 2020, 10(12), 494; https://doi.org/10.3390/metabo10120494 - 01 Dec 2020
Cited by 4 | Viewed by 1364
Abstract
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorectal cancer organoids by liquid [...] Read more.
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorectal cancer organoids by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) facing the challenge of capturing metabolic information from a minimal sample amount (<500 cells/injection) in the presence of an extracellular matrix (ECM). The best procedure of the tested protocols included ultrasonic metabolite extraction with acetonitrile/methanol/water (2:2:1, v/v/v) without ECM removal. To eliminate ECM-derived background signals, we implemented a data filtering procedure based on the p-value and fold change cut-offs, which retained features with signal intensities >120% compared to matrix-derived signals present in blank samples. As a proof-of-concept, the method was applied to examine the early metabolic response of colorectal cancer organoids to 5-fluorouracil treatment. Statistical analysis revealed dose-dependent changes in the metabolic profiles of treated organoids including elevated levels of 2′-deoxyuridine, 2′-O-methylcytidine, inosine and 1-methyladenosine and depletion of 2′-deoxyadenosine and specific phospholipids. In accordance with the mechanism of action of 5-fluorouracil, changed metabolites are mainly involved in purine and pyrimidine metabolism. The novel protocol provides a first basis for the assessment of metabolic drug response phenotypes in 3D organoid models. Full article
(This article belongs to the Special Issue Metabolomics Methodologies and Applications II)
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Article
Resting Energy Expenditure of Physically Active Boys in Southeastern Poland—The Accuracy and Validity of Predictive Equations
Metabolites 2020, 10(12), 493; https://doi.org/10.3390/metabo10120493 - 01 Dec 2020
Cited by 1 | Viewed by 801
Abstract
Optimization of energy intake in the diet of young athletes is of primary importance. In addition to the energy expenditure associated with their body development, the demand resulting from intensive physical activity also increases. The aim of this study was to compare the [...] Read more.
Optimization of energy intake in the diet of young athletes is of primary importance. In addition to the energy expenditure associated with their body development, the demand resulting from intensive physical activity also increases. The aim of this study was to compare the accuracy of formulas commonly used for resting energy expenditure (REE) calculations with values obtained from measurements using indirect calorimetry among male children and adolescents practicing football. The study was conducted among 184 boys aged 9 to 17 using a calorimeter and a device for assessing body composition by means of electrical bioimpedance using a segment analyzer. The mean error ranged from −477 kcal/d by the Maffeis formula to −182 kcal/d for the Institute of Medicine of the National Academies (IMNA) formula. A statistically significant difference was found for all formulas in the calculated value in relation to the measured REE value (p < 0.0001). Most “ready-to-use” formulas underestimate REE, which can be a risk in determining the total energy demand in a group that requires more calories, especially when due to intensive growth and development and the expenditure associated with regular training and increased physical activity. Full article
(This article belongs to the Special Issue Effect of Exercise on Energy Metabolism)
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Review
Integrative Metabolomics to Identify Molecular Signatures of Responses to Vaccines and Infections
Metabolites 2020, 10(12), 492; https://doi.org/10.3390/metabo10120492 - 30 Nov 2020
Cited by 8 | Viewed by 1580
Abstract
Approaches to the identification of metabolites have progressed from early biochemical pathway evaluation to modern high-dimensional metabolomics, a powerful tool to identify and characterize biomarkers of health and disease. In addition to its relevance to classic metabolic diseases, metabolomics has been key to [...] Read more.
Approaches to the identification of metabolites have progressed from early biochemical pathway evaluation to modern high-dimensional metabolomics, a powerful tool to identify and characterize biomarkers of health and disease. In addition to its relevance to classic metabolic diseases, metabolomics has been key to the emergence of immunometabolism, an important area of study, as leukocytes generate and are impacted by key metabolites important to innate and adaptive immunity. Herein, we discuss the metabolomic signatures and pathways perturbed by the activation of the human immune system during infection and vaccination. For example, infection induces changes in lipid (e.g., free fatty acids, sphingolipids, and lysophosphatidylcholines) and amino acid pathways (e.g., tryptophan, serine, and threonine), while vaccination can trigger changes in carbohydrate and bile acid pathways. Amino acid, carbohydrate, lipid, and nucleotide metabolism is relevant to immunity and is perturbed by both infections and vaccinations. Metabolomics holds substantial promise to provide fresh insight into the molecular mechanisms underlying the host immune response. Its integration with other systems biology platforms will enhance studies of human health and disease. Full article
(This article belongs to the Special Issue Integrative-Metabolomics in Epidemiological Studies)
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Article
Serum Metabolite Biomarkers for Predicting Residual Feed Intake (RFI) of Young Angus Bulls
Metabolites 2020, 10(12), 491; https://doi.org/10.3390/metabo10120491 - 30 Nov 2020
Cited by 6 | Viewed by 1103
Abstract
Residual feed intake (RFI) is a feed efficiency measure commonly used in the livestock industry to identify animals that efficiently/inefficiently convert feed into meat or body mass. Selection for low-residual feed intake (LRFI), or feed efficient animals, is gaining popularity among beef producers [...] Read more.
Residual feed intake (RFI) is a feed efficiency measure commonly used in the livestock industry to identify animals that efficiently/inefficiently convert feed into meat or body mass. Selection for low-residual feed intake (LRFI), or feed efficient animals, is gaining popularity among beef producers due to the fact that LRFI cattle eat less and produce less methane per unit weight gain. RFI is a difficult and time-consuming measure to perform, and therefore a simple blood test that could distinguish high-RFI (HRFI) from LRFI animals (early on) would potentially benefit beef farmers in terms of optimizing production or selecting which animals to cull or breed. Using three different metabolomics platforms (nuclear magnetic resonance (NMR) spectrometry, liquid chromatography-tandem mass spectrometry (LC-MS/MS), and inductively coupled plasma mass spectrometry (ICP-MS)) we successfully identified serum biomarkers for RFI that could potentially be translated to an RFI blood test. One set of predictive RFI biomarkers included formate and leucine (best for NMR), and another set included C4 (butyrylcarnitine) and LysoPC(28:0) (best for LC-MS/MS). These serum biomarkers have high sensitivity and specificity (AUROC > 0.85), for distinguishing HRFI from LRFI animals. These results suggest that serum metabolites could be used to inexpensively predict and categorize bovine RFI values. Further validation using a larger, more diverse cohort of cattle is required to confirm these findings. Full article
(This article belongs to the Section Animal Metabolism)
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Addendum
Addendum: An Optimised Dual Extraction Method for the Simultaneous and Accurate Analysis of Polar Metabolites and Lipids Carried out on Single Biological Samples. Metabolites 2020, 10, 338
Metabolites 2020, 10(12), 490; https://doi.org/10.3390/metabo10120490 - 30 Nov 2020
Cited by 1 | Viewed by 447
Abstract
The authors wish to make the following comment to the paper [...] Full article
(This article belongs to the Section Metabolomic Profiling Technology)
Article
Flux Coupling and the Objective Functions’ Length in EFMs
Metabolites 2020, 10(12), 489; https://doi.org/10.3390/metabo10120489 - 28 Nov 2020
Viewed by 595
Abstract
Structural analysis of constraint-based metabolic network models attempts to find the network’s properties by searching for subsets of suitable modes or Elementary Flux Modes (EFMs). One useful approach is based on Linear Program (LP) techniques, which introduce an objective function to convert the [...] Read more.
Structural analysis of constraint-based metabolic network models attempts to find the network’s properties by searching for subsets of suitable modes or Elementary Flux Modes (EFMs). One useful approach is based on Linear Program (LP) techniques, which introduce an objective function to convert the stoichiometric and thermodynamic constraints into a linear program (LP), using additional constraints to generate different nontrivial modes. This work introduces FLFS-FC (Fixed Length Function Sampling with Flux Coupling), a new approach to increase the efficiency of generation of large sets of different EFMs for the network. FLFS-FC is based on the importance of the length of the objective functions used in the associated LP problem and the imposition of additional negative constraints. Our proposal overrides some of the known drawbacks associated with the EFM extraction, such as the appearance of unfeasible problems or multiple repeated solutions arising from different LP problems. Full article
(This article belongs to the Special Issue Computational Biology for Metabolic Modelling)
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