Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 1 hour 16 min ago

Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model.

Sun, 03/01/2021 - 12:12
Related Articles Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model. Toxicol Appl Pharmacol. 2020 Dec 30;:115390 Authors: Rawls KD, Dougherty BV, Vinnakota KC, Pannala VR, Wallqvist A, Kolling GL, Papin JA Abstract The kidneys are metabolically active organs with importance in several physiological tasks such as the secretion of soluble wastes into the urine and synthesizing glucose and oxidizing fatty acids for energy in fasting (non-fed) conditions. Once damaged, the metabolic capability of the kidneys becomes altered. Here, we define metabolic tasks in a computational modeling framework to capture kidney function in an update to the iRno network reconstruction of rat metabolism using literature-based evidence. To demonstrate the utility of iRno for predicting kidney function, we exposed primary rat renal proximal tubule epithelial cells to four compounds with varying levels of nephrotoxicity (acetaminophen, gentamicin, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six and twenty-four hours, and collected transcriptomics and metabolomics data to measure the metabolic effects of compound exposure. For the transcriptomics data, we observed changes in fatty acid metabolism and amino acid metabolism, as well as changes in existing markers of kidney function such as Clu (clusterin). The iRno metabolic network reconstruction was used to predict alterations in these same pathways after integrating transcriptomics data and was able to distinguish between select compound-specific effects on the proximal tubule epithelial cells. Genome-scale metabolic network reconstructions with coupled omics data can be used to predict changes in metabolism as a step towards identifying novel metabolic biomarkers of kidney function and dysfunction. PMID: 33387578 [PubMed - as supplied by publisher]

Altered gut microbial metabolism of essential nutrients in primary sclerosing cholangitis.

Sun, 03/01/2021 - 12:12
Related Articles Altered gut microbial metabolism of essential nutrients in primary sclerosing cholangitis. Gastroenterology. 2020 Dec 30;: Authors: Kummen M, Thingholm LB, Rühlemann MC, Holm K, Hansen SH, Moitinho-Silva L, Liwinski T, Zenouzi R, Storm-Larsen C, Midttun Ø, McCann A, Ueland PM, Høivik ML, Vesterhus M, Trøseid M, Laudes M, Lieb W, Karlsen TH, Bang C, Schramm C, Franke A, Hov JR Abstract BACKGROUND AND AIMS: To influence host and disease phenotype, compositional microbiome changes, which have been demonstrated in patients with primary sclerosing cholangitis (PSC), must be accompanied by functional changes. We therefore aimed to characterize the genetic potential of the gut microbiome in PSC compared to healthy controls (HCs) and inflammatory bowel disease (IBD). METHODS: Fecal DNA from two cohorts (one Norwegian and one German), in total comprising 136 patients with PSC (58% with IBD), 158 HCs and 93 IBD patients without PSC were subjected to metagenomic shotgun sequencing, generating 17 billion paired end sequences, which were processed using HUMAnN2 and MetaPhlAn2, and analyzed using generalized linear models and random effects meta-analyses. RESULTS: PSC patients had fewer microbial genes compared to HC (P<.0001). Compared to HC, PSC patients showed enrichment and increased prevalence of Clostridium species, and a depletion of e.g., Eubacterium spp. and Ruminococcus obeum. Patients with PSC showed marked differences in the abundance of genes related to vitamin B6 synthesis and branched chain amino acid (BCAA) synthesis (Qfdr<.05). Targeted metabolomics of plasma from an independent set of PSC patients and controls found reduced concentrations of vitamin B6 and BCAAs in PSC (P<.0001), which strongly associated with reduced liver transplantation-free survival (log-rank P<.001). No taxonomic or functional differences were detected between PSC patients with and without IBD. CONCLUSION: The gut microbiome of PSC patients exhibits large functional differences compared to HC, including microbial metabolism of essential nutrients. Alterations in related circulating metabolites associated with disease course, suggesting that microbial functions may be relevant for the disease process in PSC. PMID: 33387530 [PubMed - as supplied by publisher]

Comparative metabolomics reveals key pathways associated with the synergistic activity of polymyxin B and rifampicin combination against multidrug-resistant Acinetobacter baumannii.

Sun, 03/01/2021 - 12:12
Related Articles Comparative metabolomics reveals key pathways associated with the synergistic activity of polymyxin B and rifampicin combination against multidrug-resistant Acinetobacter baumannii. Biochem Pharmacol. 2020 Dec 30;:114400 Authors: Zhao J, Han ML, Zhu Y, Lin YW, Wang YW, Lu J, Hu Y, Tony Zhou Q, Velkov T, Li J Abstract Multidrug-resistant (MDR) Acinetobacter baumannii presents a critical challenge to human health worldwide and polymyxins are increasingly used as a last-line therapy. Due to the rapid emergence of resistance during polymyxin monotherapy, synergistic combinations (e.g. with rifampicin) are recommended to treat A. baumannii infections. However, most combination therapies are empirical, owing to a dearth of understanding on the mechanism of synergistic antibacterial killing. In the present study, we employed metabolomics to investigate the synergy mechanism of polymyxin B-rifampicin against A. baumannii AB5075, an MDR clinical isolate. The metabolomes of A. baumannii AB5075 were compared at 1 and 4 h following treatments with polymyxin B alone (0.75 mg/L, i.e. 3×MIC), rifampicin alone (1 mg/L, i.e. 0.25×MIC) and their combination. Polymyxin B monotherapy significantly perturbed glycerophospholipid and fatty acid metabolism at 1 h, reflecting its activity on bacterial outer membrane. Rifampicin monotherapy significantly perturbed glycerophospholipid, nucleotide and amino acid metabolism, which are related to the inhibition of RNA synthesis. The combination treatment significantly perturbed the metabolism of nucleotides, amino acids, fatty acids and glycerophospholipids at 1 and 4 h. Notably, the intermediate metabolite pools from pentose phosphate pathway were exclusively enhanced by the combination, while most metabolites from the nucleotide and amino acid biosynthesis pathways were significantly decreased. Overall, the synergistic activity of the combination was initially driven by polymyxin B which impacted pathways associated with outer membrane biogenesis; and subsequent effects were mainly attributed to rifampicin via the inhibition of RNA synthesis. This study is the first to reveal the synergistic killing mechanism of the polymyxin-rifampicin combination against polymyxin-susceptible MDR A. baumannii at the network level. Our findings provide new mechanistic insights for optimizing this synergistic combination in patients. PMID: 33387481 [PubMed - as supplied by publisher]

Stem cell-based models and therapies: a key approach into schizophrenia treatment.

Sun, 03/01/2021 - 12:12
Related Articles Stem cell-based models and therapies: a key approach into schizophrenia treatment. Cell Tissue Bank. 2021 Jan 02;: Authors: Larijani B, Parhizkar Roudsari P, Hadavandkhani M, Alavi-Moghadam S, Rezaei-Tavirani M, Goodarzi P, Sayahpour FA, Mohamadi-Jahani F, Arjmand B Abstract Psychiatric disorders such as schizophrenia can generate distress and disability along with heavy costs on individuals and health care systems. Different genetic and environmental factors play a pivotal role in the appearance of the mentioned disorders. Since the conventional treatment options for psychiatric disorders are suboptimal, investigators are trying to find novel strategies. Herein, stem cell therapies have been recommended as novel choices. In this context, the preclinical examination of stem cell-based therapies specifically using appropriate models can facilitate passing strong filters and serious examination to ensure proper quality and safety of them as a novel treatment approach. Animal models cannot be adequately helpful to follow pathophysiological features. Nowadays, stem cell-based models, particularly induced pluripotent stem cells reflected as suitable alternative models in this field. Accordingly, the importance of stem cell-based models, especially to experiment with the regenerative medicine outcomes for schizophrenia as one of the severe typing of psychiatric disorders, is addressed here. PMID: 33387152 [PubMed - as supplied by publisher]

Salivary metabolomics for the diagnosis of periodontal diseases: a systematic review with methodological quality assessment.

Sun, 03/01/2021 - 12:12
Related Articles Salivary metabolomics for the diagnosis of periodontal diseases: a systematic review with methodological quality assessment. Metabolomics. 2021 Jan 01;17(1):1 Authors: Baima G, Iaderosa G, Citterio F, Grossi S, Romano F, Berta GN, Buduneli N, Aimetti M Abstract INTRODUCTION: Early diagnosis of periodontitis by means of a rapid, accurate and non-invasive method is highly desirable to reduce the individual and epidemiological burden of this largely prevalent disease. OBJECTIVES: The aims of the present systematic review were to examine potential salivary metabolic biomarkers and pathways associated to periodontitis, and to assess the accuracy of salivary untargeted metabolomics for the diagnosis of periodontal diseases. METHODS: Relevant studies identified from MEDLINE (PubMed), Embase and Scopus databases were systematically examined for analytical protocols, metabolic biomarkers and results from the multivariate analysis (MVA). Pathway analysis was performed using the MetaboAnalyst online software and quality assessment by means of a modified version of the QUADOMICS tool. RESULTS: Twelve studies met the inclusion criteria, with sample sizes ranging from 19 to 130 subjects. Compared to periodontally healthy individuals, valine, phenylalanine, isoleucine, tyrosine and butyrate were found upregulated in periodontitis patients in most studies; while lactate, pyruvate and N-acetyl groups were the most significantly expressed in healthy individuals. Metabolic pathways that resulted dysregulated are mainly implicated in inflammation, oxidative stress, immune activation and bacterial energetic metabolism. The findings from MVA revealed that periodontitis is characterized by a specific metabolic signature in saliva, with coefficients of determination ranging from 0.52 to 0.99. CONCLUSIONS: This systematic review summarizes candidate metabolic biomarkers and pathways related to periodontitis, which may provide opportunities for the validation of diagnostic or predictive models and the discovery of novel targets for monitoring and treating such a disease (PROSPERO CRD42020188482). PMID: 33387070 [PubMed - as supplied by publisher]

Metabolomics approach based on LC-HRMS for the fast screening of iron(II)-chelating peptides in protein hydrolysates.

Sun, 03/01/2021 - 12:12
Related Articles Metabolomics approach based on LC-HRMS for the fast screening of iron(II)-chelating peptides in protein hydrolysates. Anal Bioanal Chem. 2021 Jan 02;: Authors: Paris C, Selmeczi K, Ebel B, Stefan L, Csire G, Cakir-Kiefer C, Desobry S, Canabady-Rochelle L, Chaimbault P Abstract Production of iron-chelating peptides from protein hydrolysates requires robust and adequate screening methods to optimize their purification and subsequently valorize their potential antioxidant properties. An original methodology was developed for direct and sensitive screening of iron(II)-chelating peptides based on ion-pair reverse phase liquid chromatography (IP-RPLC) coupled to high-resolution mass spectrometry (HRMS). Peptide mixture was first added to iron(II) solution to form iron(II)-peptide complexes. Then IP-RPLC-HRMS analysis was conducted on this iron-peptide mixture and on the iron-free peptide solution for comparative mass spectra analysis. This protocol, initially applied to a range of low molecular weight standard peptides, allowed detection of [(Peptide-H)+56FeII]+ complex ion for iron(II)-chelating peptides (GGH, EAH, DAH, βAH, DMH, DTH, DSH). GGH was added in complex peptide mixtures and targeted analysis of [(GGH-H)+56FeII]+ complex showed a limit of detection (LOD) below 0.77 mg L-1 of GGH. This protocol was finally tested in combination with metabolomics software and additional digital processing for non-targeted search for iron(II)-chelating peptides. Applicability of this new screening methodology has been validated by detection of GGH as iron(II)-chelating peptide when added at 0.77 mg L-1 in casein hydrolysate. Graphical abstract. PMID: 33386417 [PubMed - as supplied by publisher]

Enteral Vitamin A for Reducing Severity of Bronchopulmonary Dysplasia: A Randomized Trial.

Sun, 03/01/2021 - 12:12
Related Articles Enteral Vitamin A for Reducing Severity of Bronchopulmonary Dysplasia: A Randomized Trial. Pediatrics. 2021 Jan;147(1): Authors: Rakshasbhuvankar AA, Simmer K, Patole SK, Stoecklin B, Nathan EA, Clarke MW, Pillow JJ Abstract BACKGROUND AND OBJECTIVES: Evidence suggests that intramuscular vitamin A reduces the risk of bronchopulmonary dysplasia (BPD) in preterm infants. Our objective was to compare enteral water-soluble vitamin A with placebo supplementation to reduce the severity of BPD in extremely preterm infants. METHODS: We conducted a double-blind randomized controlled trial in infants <28 weeks' gestation who were to receive either enteral water-soluble vitamin A (5000 IU per day) or a placebo. Supplementation was started within 24 hours of introduction of feeds and continued until 34 weeks' postmenstrual age (PMA). The primary outcome was the severity of BPD, assessed by using the right shift of the pulse oximeter saturation versus the inspired oxygen pressure curve. RESULTS: A total of 188 infants were randomly assigned. The mean ± SD birth weight (852 ± 201 vs 852 ± 211 g) and gestation (25.8 ± 1.49 vs 26.0 ± 1.39 weeks) were comparable between the vitamin A and placebo groups. There was no difference in the right shift (median [25th-75th percentiles]) of the pulse oximeter saturation versus inspired oxygen pressure curve (in kilopascals) between the vitamin A (11.1 [9.5-13.7]) and placebo groups (10.7 [9.5-13.1]) (P = .73). Enteral vitamin A did not affect diagnosis of BPD or other clinical outcomes. Plasma retinol levels were significantly higher in the vitamin A group versus the placebo group on day 28 and at 34 weeks' PMA. CONCLUSIONS: Enteral water-soluble vitamin A supplementation improves plasma retinol levels in extremely preterm infants but does not reduce the severity of BPD. PMID: 33386338 [PubMed - as supplied by publisher]

Soil assessment after chemical accidents using metabolic profiling and microbial community evaluation.

Sat, 02/01/2021 - 15:06
Related Articles Soil assessment after chemical accidents using metabolic profiling and microbial community evaluation. Chemosphere. 2020 Dec 18;268:129362 Authors: Kim N, Ahn Y, Jo J, Pyo H, Lee J, Choi J Abstract This study investigated the effects of accidental contamination of soils with phenol, toluene, nitric acid, and hydrogen fluoride (HF) by simulating chemical leakage in the soil with/without rain and characterizing the resulting metabolites and microbial. In the case of acid leakage, pH and cation exchange capacity were decreased, and the content of fluoride ion was increased in case of HF leakage. Using mass spectrometry-based metabolomics analysis, phytosphingosine was detected as a distinguishing metabolite in soils contaminated with phenol and HF in rain conditions. Microbial communities were identified by 16s rRNA metagenome sequencing. Sphingomonas was one of the dominant species in soils contaminated with phenol and HF. These results suggest that phytosphingosine and Sphingomonas might be used as biomarkers to evaluate the status of soils contaminated with phenol or HF. Under simulated rain conditions, the species alpha-diversity index of soil microbes and the physicochemical properties of the soil indicated values close to those of the uncontaminated soil. Rain played an important role in the recovery of microbial and metabolic profiles after chemical accidents. Metabolic profiling and microbial community analysis can serve as a diagnostic tool for ecotoxicological research at chemical accident sites. PMID: 33385834 [PubMed - as supplied by publisher]

Combination of UHPLC-MS/MS-molecular networking approach and FTICR-MS for the metabolic profiling of Saccharomyces cerevisiae.

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Related Articles Combination of UHPLC-MS/MS-molecular networking approach and FTICR-MS for the metabolic profiling of Saccharomyces cerevisiae. J Pharm Biomed Anal. 2020 Dec 19;195:113857 Authors: Perruchon O, Schmitz-Afonso I, Grondin C, Casaregola S, Afonso C, Elomri A Abstract Natural products are a reliable source of bioactive molecules and represent an industrial and pharmaceutical stake. Indeed, the model yeast species Saccharomyces cerevisiae is a well-known eukaryotic organism largely used as a biotechnological tool, but still a topical subject of study. In this work, the exploration of Saccharomyces cerevisiae is taken further through an untargeted metabolomics workflow. The aim is to enrich databases and bring new information about the standard S. cerevisiae strain in a given medium. Analytical methods and bioinformatics tools were combined in a high-throughput methodology useable to dereplicate many types of biological extracts and cartography secondary metabolites. Ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analyses were carried out and spectral data were pre-processed to build molecular networks. Annotations were attributed to compounds through comparison with databases and manual investigation of networks. Ultra-high-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) brought additional information thanks to a higher dynamic range and enhanced UHPLC-MS/MS results by unveiling ambiguities and bringing accurate molecular formulae. Therefore, accurate and reliable annotated features resulted from the UHPLC-MS/MS data while FTICR-MS provided an overall cartography of metabolites thanks to van Krevelen diagrams. Various small molecules such as amino acids derivatives and indole alkaloids have been determined for the first time in this yeast. The complementarity of FTICR-MS and UHPLC-MS/MS for secondary metabolite annotation brought this new mapping of S. cerevisiae. PMID: 33385718 [PubMed - as supplied by publisher]

SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics.

Sat, 02/01/2021 - 15:06
Related Articles SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics. iScience. 2021 Jan 22;24(1):101925 Authors: Jaiswal SK, Agarwal SM, Thodum P, Sharma VK Abstract In addition to being pivotal for the host health, the skin microbiome possesses a large reservoir of metabolic enzymes, which can metabolize molecules (cosmetics, medicines, pollutants, etc.) that form a major part of the skin exposome. Therefore, to predict the complete metabolism of any molecule by skin microbiome, a curated database of metabolic enzymes (1,094,153), reactions, and substrates from ∼900 bacterial species from 19 different skin sites were used to develop "SkinBug." It integrates machine learning, neural networks, and chemoinformatics methods, and displays a multiclass multilabel accuracy of up to 82.4% and binary accuracy of up to 90.0%. SkinBug predicts all possible metabolic reactions and associated enzymes, reaction centers, skin microbiome species harboring the enzyme, and the respective skin sites. Thus, SkinBug will be an indispensable tool to predict xenobiotic/biotic metabolism by skin microbiome and will find applications in exposome and microbiome studies, dermatology, and skin cancer research. PMID: 33385118 [PubMed]

Metabolite Fingerprinting of Kersting's Groundnut [Macrotyloma geocarpum (Harms) Maréchal & Baudet] Seeds Using UPLC-qTOF-MS Reveals the Nutraceutical and Antioxidant Potentials of the Orphan Legume.

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Related Articles Metabolite Fingerprinting of Kersting's Groundnut [Macrotyloma geocarpum (Harms) Maréchal & Baudet] Seeds Using UPLC-qTOF-MS Reveals the Nutraceutical and Antioxidant Potentials of the Orphan Legume. Front Nutr. 2020;7:593436 Authors: Tsamo AT, Mohammed M, Dakora FD Abstract The identification and subsequent quantification of phenolic compounds in plants is the first step toward harnessing their associated nutritional and health benefits. Due to their diverse phenolic compound compositions, grain legumes are known for their high nutritional and health values. The aim of this study was to assess the inter-variations in chemical composition, phytochemical content, and antioxidant capacity of seed extracts from eight Kersting's groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] landraces. The chemical profiles were evaluated using UPLC-qTOF-MS. Total phenolics and flavonoids content were determined by the Folin-Ciocalteu and aluminum chloride methods, respectively. The antioxidant capacities in the forms of DPPH and ABTS were evaluated using spectrophotometric methods. Principal component analysis was used to define similarities/differences between the landraces. Based on untargeted metabolomics analysis, 57 metabolites were identified, with phenolics, triterpenes, fatty acids, and sphingolipids being the most predominant. The results showed that the black seeded KG1 (Puffeun) had the highest total phenolic (9.44 mg GAE/g) and flavonoid (3.01 mg QE/g) contents, as well as antioxidant capacity (9.17 μg/mL and 18.44 μg/mL based on DDPH and ABTS assays, respectively). The concentrations of ferulic acid hexoside, procyanidin B2, eryodictyiol-7-rutinoside and quercetin pentoside ranged from 51.78-441.31, 1.86-18.25, 3.26-13.95 to 5.44-63.85 μg/mg, respectively. This study presents a useful report on the phytochemical characterization of Kersting's groundnuts and shows that the grains can be used as a source of nutraceuticals for human consumption. PMID: 33385005 [PubMed]

The Implications of PDK1-4 on Tumor Energy Metabolism, Aggressiveness and Therapy Resistance.

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Related Articles The Implications of PDK1-4 on Tumor Energy Metabolism, Aggressiveness and Therapy Resistance. Front Oncol. 2020;10:583217 Authors: Atas E, Oberhuber M, Kenner L Abstract A metabolic shift from oxidative phosphorylation (OXPHOS) to glycolysis-known as the Warburg effect-is characteristic for many cancers. It gives the cancer cells a survival advantage in the hypoxic tumor microenvironment and protects them from cytotoxic effects of oxidative damage and apoptosis. The main regulators of this metabolic shift are the pyruvate dehydrogenase complex and pyruvate dehydrogenase kinase (PDK) isoforms 1-4. PDK is known to be overexpressed in several cancers and is associated with bad prognosis and therapy resistance. Whereas the expression of PDK1-3 is tissue specific, PDK4 expression is dependent on the energetic state of the whole organism. In contrast to other PDK isoforms, not only oncogenic, but also tumor suppressive functions of PDK4 have been reported. In tumors that profit from high OXPHOS and high de novo fatty acid synthesis, PDK4 can have a protective effect. This is the case for prostate cancer, the most common cancer in men, and makes PDK4 an interesting therapeutic target. While most work is focused on PDK in tumors characterized by high glycolytic activity, little research is devoted to those cases where PDK4 acts protective and is therefore highly needed. PMID: 33384955 [PubMed]

Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks.

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Related Articles Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J. 2021;19:72-85 Authors: Desmet S, Brouckaert M, Boerjan W, Morreel K Abstract Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed. PMID: 33384856 [PubMed]

Molecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics.

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Related Articles Molecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics. Hortic Res. 2021 Jan 01;8(1):12 Authors: Berni R, Charton S, Planchon S, Legay S, Romi M, Cantini C, Cai G, Hausman JF, Renaut J, Guerriero G Abstract Sweet cherry (Prunus avium L.) is a stone fruit widely consumed and appreciated for its organoleptic properties, as well as its nutraceutical potential. We here investigated the characteristics of six non-commercial Tuscan varieties of sweet cherry maintained at the Regional Germplasm Bank of the CNR-IBE in Follonica (Italy) and sampled ca. 60 days post-anthesis over three consecutive years (2016-2017-2018). We adopted an approach merging genotyping and targeted gene expression profiling with metabolomics. To complement the data, a study of the soluble proteomes was also performed on two varieties showing the highest content of flavonoids. Metabolomics identified the presence of flavanols and proanthocyanidins in highest abundance in the varieties Morellona and Crognola, while gene expression revealed that some differences were present in genes involved in the phenylpropanoid pathway during the 3 years and among the varieties. Finally, proteomics on Morellona and Crognola showed variations in proteins involved in stress response, primary metabolism and cell wall expansion. To the best of our knowledge, this is the first multi-pronged study focused on Tuscan sweet cherry varieties providing insights into the differential abundance of genes, proteins and metabolites. PMID: 33384418 [PubMed]

Plasma and serum oxylipin, endocannabinoid, bile acid, steroid, fatty acid and nonsteroidal anti-inflammatory drug quantification in a 96-well plate format.

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Related Articles Plasma and serum oxylipin, endocannabinoid, bile acid, steroid, fatty acid and nonsteroidal anti-inflammatory drug quantification in a 96-well plate format. Anal Chim Acta. 2021 Jan 25;1143:189-200 Authors: Pedersen TL, Gray IJ, Newman JW Abstract The goal of this research was to develop a high-throughput, cost-effective method for metabolic profiling of lipid mediators and hormones involved in the regulation of inflammation and energy metabolism, along with polyunsaturated fatty acids and common over-the-counter non-steroidal anti-inflammatory drugs (NSAIDs). We describe a 96-well plate protein precipitation and filtration procedure for 50 μL of plasma or serum in the presence of 37 deuterated analogs and 2 instrument internal standards. Data is acquired in two back-to-back UPLC-MS/MS analyses using electrospray ionization with positive/negative switching and scheduled multiple reaction monitoring for the determination of 145 compounds, including oxylipins, endocannabinoids and like compounds, bile acids, glucocorticoids, sex steroids, polyunsaturated fatty acids, and 3 NSAIDs. Intra- and inter-batch variability was <25% for >70% of metabolites above the LOQ in both matrices, but higher inter-batch variability was observed for serum oxylipins and some bile acids. Results for NIST Standard Reference Material 1950, compared favorably with the 20 certified metabolite values covered by this assay, and we provide new data for oxylipins, N-acylethanolamides, glucocorticoids, and 17-hydroxy-progesterone in this material. Application to two independent cohorts of elderly men and women showed the routine detection of 86 metabolites, identified fasting state influences on essential fatty acid-derived oxylipins, N-acylethanolamides and conjugated bile acids, identified rare presence of high and low testosterone levels and the presence of NSAIDs in ∼10% of these populations. The described method appears valuable for investigations in large cohort studies to provide insight into metabolic cross-talk between the array of mediators assessed here. PMID: 33384117 [PubMed - in process]

Anion exchange chromatography - Mass spectrometry for monitoring multiple quality attributes of erythropoietin biopharmaceuticals.

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Related Articles Anion exchange chromatography - Mass spectrometry for monitoring multiple quality attributes of erythropoietin biopharmaceuticals. Anal Chim Acta. 2021 Jan 25;1143:166-172 Authors: van Schaick G, Gstöttner C, Büttner A, Reusch D, Wuhrer M, Domínguez-Vega E Abstract Assessment of critical quality attributes of the biopharmaceutical erythropoietin (EPO) prior to product release requires the use of several analytical methods. We developed an MS-compatible anion exchange (AEX) method for monitoring multiple quality attributes of EPO biopharmaceuticals. AEX was performed using a stationary phase with quaternary ammonium functional groups and a pH gradient for elution. Baseline separation of charge variants and high-quality MS data were achieved using 30 mM ammonium formate pH 5.5 and 30 mM formic acid pH 2.5 as mobile phases. In a single experiment, assessment of critical quality attributes, such as charge heterogeneity, sialic acid content and number of N-acetyllactosamine units, was possible while providing additional information on other modifications such as O-acetylation and deamidation. In addition, good repeatability and robustness for the relative areas of the individual glycoforms and average number of Neu5Ac per EPO molecule were observed. The results were comparable to common pharmacopeia and standard methods with the advantage of requiring fewer analytical methods and less sample treatment saving time and costs. PMID: 33384114 [PubMed - in process]

Single cell metabolomics using mass spectrometry: Techniques and data analysis.

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Related Articles Single cell metabolomics using mass spectrometry: Techniques and data analysis. Anal Chim Acta. 2021 Jan 25;1143:124-134 Authors: Liu R, Yang Z Abstract Mass spectrometry (MS) based techniques are gaining popularity for metabolomics research due to their high sensitivity, wide detection range, and capability of molecular identification. Utilizing such powerful technique to explore the cellular metabolism at the single cell level not only appreciates the subtle cell-to-cell difference (i.e., cell heterogeneity), but also gains biological merits corresponding to individual cells or small cell subpopulations. In this review article, we first briefly summarize recent advances in single cell MS experimental techniques, and then emphasize on the single cell metabolomics data analysis approaches. Through implementation of statistical analysis and more advanced data analysis methods, single cell metabolomics is expected to find more potential applications in the translational and clinical fields in the future. PMID: 33384110 [PubMed - in process]

Effects of a Synbiotic Formula on Functional Bowel Disorders and Gut Microbiota Profile during Long-Term Home Enteral Nutrition (LTHEN): A Pilot Study.

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Related Articles Effects of a Synbiotic Formula on Functional Bowel Disorders and Gut Microbiota Profile during Long-Term Home Enteral Nutrition (LTHEN): A Pilot Study. Nutrients. 2020 Dec 29;13(1): Authors: D'Onofrio V, Del Chierico F, Belci P, Vernocchi P, Quagliariello A, Reddel S, Conta G, Mancino MV, Fadda M, Scigliano MC, Morelli R, De Francesco A, Guagnini F, Fassio F, Galletti R, Putignani L Abstract Long-term enteral nutrition (LTEN) can induce gut microbiota (GM) dysbiosis and gastrointestinal related symptoms, such as constipation or diarrhoea. To date, the treatment of constipation is based on the use of laxatives and prebiotics. Only recently have probiotics and synbiotics been considered, the latter modulating the GM and regulating intestinal functions. This randomized open-label intervention study evaluated the effects of synbiotic treatment on the GM profile, its functional activity and on intestinal functions in long-term home EN (LTHEN) patients. Twenty LTHEN patients were recruited to take enteral formula plus one sachet/day of synbiotic (intervention group, IG) or enteral formula (control group, CG) for four months and evaluated for constipation, stool consistency, and GM and metabolite profiles. In IG patients, statistically significant reduction of constipation and increase of stool consistency were observed after four months (T1), compared to CG subjects. GM ecology analyses revealed a decrease in the microbial diversity of both IC and CG groups. Biodiversity increased at T1 for 5/11 IG patients and Methanobrevibacter was identified as the biomarker correlated to the richness increase. Moreover, the increase of short chain fatty acids and the reduction of harmful molecules have been correlated to synbiotic administration. Synbiotics improve constipation symptoms and influences Methanobrevibacter growth in LTHEN patients. PMID: 33383954 [PubMed - in process]

Holistic Metabolomic Laboratory-Developed Test (LDT): Development and Use for the Diagnosis of Early-Stage Parkinson's Disease.

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Related Articles Holistic Metabolomic Laboratory-Developed Test (LDT): Development and Use for the Diagnosis of Early-Stage Parkinson's Disease. Metabolites. 2020 Dec 29;11(1): Authors: Lokhov PG, Maslov DL, Lichtenberg S, Trifonova OP, Balashova EE Abstract A laboratory-developed test (LDT) is a type of in vitro diagnostic test that is developed and used within a single laboratory. The holistic metabolomic LDT integrating the currently available data on human metabolic pathways, changes in the concentrations of low-molecular-weight compounds in the human blood during diseases and other conditions, and their prevalent location in the body was developed. That is, the LDT uses all of the accumulated metabolic data relevant for disease diagnosis and high-resolution mass spectrometry with data processing by in-house software. In this study, the LDT was applied to diagnose early-stage Parkinson's disease (PD), which currently lacks available laboratory tests. The use of the LDT for blood plasma samples confirmed its ability for such diagnostics with 73% accuracy. The diagnosis was based on relevant data, such as the detection of overrepresented metabolite sets associated with PD and other neurodegenerative diseases. Additionally, the ability of the LDT to detect normal composition of low-molecular-weight compounds in blood was demonstrated, thus providing a definition of healthy at the molecular level. This LDT approach as a screening tool can be used for the further widespread testing for other diseases, since 'omics' tests, to which the metabolomic LDT belongs, cover a variety of them. PMID: 33383698 [PubMed]

Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor.

Sat, 02/01/2021 - 12:06
Related Articles Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor. Sci Rep. 2020 10 01;10(1):16353 Authors: Snow SJ, Broniowska K, Karoly ED, Henriquez AR, Phillips PM, Ledbetter AD, Schladweiler MC, Miller CN, Gordon CJ, Kodavanti UP Abstract The influence of maternal high-fat diet (HFD) on metabolic response to ozone was examined in Long-Evans rat offspring. F0 females were fed control diet (CD; 10%kcal from fat) or HFD (60%kcal from fat) starting at post-natal day (PND) 30. Rats were bred on PND 72. Dietary regimen was maintained until PND 30 when all offspring were switched to CD. On PND 40, F1 offspring (n = 10/group/sex) were exposed to air or 0.8 ppm ozone for 5 h. Serum samples were collected for global metabolomic analysis (n = 8/group/sex). Offspring from HFD dams had increased body fat and weight relative to CD. Metabolomic analysis revealed significant sex-, diet-, and exposure-related changes. Maternal HFD increased free fatty acids and decreased phospholipids (male > female) in air-exposed rats. Microbiome-associated histidine and tyrosine metabolites were increased in both sexes, while 1,5-anhydroglucitol levels decreased in males indicating susceptibility to insulin resistance. Ozone decreased monohydroxy fatty acids and acyl carnitines and increased pyruvate along with TCA cycle intermediates in females (HFD > CD). Ozone increased various amino acids, polyamines, and metabolites of gut microbiota in HFD female offspring indicating gut microbiome alterations. Collectively, these data suggest that maternal HFD increases offspring susceptibility to metabolic alterations in a sex-specific manner when challenged with environmental stressors. PMID: 33004997 [PubMed - in process]

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