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: 55 min 27 sec ago

Extending the Scope of 1H NMR Spectroscopy for the Analysis of Cellular Coenzyme A and Acetyl Coenzyme A.

Sat, 05/01/2019 - 14:54
Related Articles Extending the Scope of 1H NMR Spectroscopy for the Analysis of Cellular Coenzyme A and Acetyl Coenzyme A. Anal Chem. 2019 Jan 04;: Authors: Gowda GAN, Abell L, Tian R Abstract Coenzyme A (CoA) and acetyl-coenzyme A (acetyl-CoA) are ubiquitous cellular molecules, which mediate hundreds of anabolic and catabolic reactions including energy metabolism. Highly sensitive methods including absorption spectroscopy and mass spectrometry enable their analysis, albeit with many limitations. To date, however, NMR spectroscopy has not been used to analyze these important molecules. Building on our recent efforts, which enabled simultaneous analysis of a large number of metabolites in tissue and blood including many coenzymes and antioxidants [Anal Chem. 2016, 88:4817-24; ibid 2017, 89:4620-4627], we describe here a new method for identification and quantitation of CoA and acetyl-CoA ex vivo in tissue. Using mouse heart, kidney, liver, brain and skeletal tissue, we show that a simple 1H NMR experiment can simultaneously measure these molecules. Identification of the two species involved a comprehensive analysis of the different tissue types using 1D and 2D NMR, in combination with spectral databases for standards, as well as spiking with authentic compounds. Time dependent studies showed that while the acetyl-CoA levels remain unaltered, CoA levels diminish by more than 50% within 24 h, which indicates that CoA is labile in solution; however, degassing the sample with helium gas halted its oxidation. Further, interestingly, we also identified endogenous coenzyme A glutathione disulfide (CoA-S-S-G) in tissue for the first time by NMR and show that CoA, when oxidized in tissue extract also forms the same disulfide metabolite. The new ability to simultaneously visualize absolute concentrations of CoA, acetyl-CoA and endogenous CoA-S-S-G along with redox coenzymes (NAD+, NADH, NADP+, NADPH), energy coenzymes (ATP, ADP, AMP), antioxidants (GSH, GSSG) and a vast pool of other metabolites using a single 1D NMR spectrum offers a new avenue in the metabolomics field for investigation of cellular function in health and disease. PMID: 30608643 [PubMed - as supplied by publisher]

Methionine Supply During Late-Gestation Triggers Offspring Sex-Specific Divergent Changes in Metabolic and Epigenetic Signatures in Bovine Placenta.

Sat, 05/01/2019 - 14:54
Related Articles Methionine Supply During Late-Gestation Triggers Offspring Sex-Specific Divergent Changes in Metabolic and Epigenetic Signatures in Bovine Placenta. J Nutr. 2019 Jan 04;: Authors: Batistel F, Alharthi AS, Yambao RRC, Elolimy AA, Pan YX, Parys C, Loor JJ Abstract Background: Nonruminant male and female offspring respond differently to gestational nutrition, with placenta contributing to the underlying mechanisms. However, similar data are lacking in large ruminants. Objectives: The aim of this study was to investigate the impact of methionine supply during late-gestation on metabolism and DNA methylation in placenta from cows carrying male or female calves. Methods: During the last 28 d of pregnancy, cows were individually fed a control diet (CON) or the control diet plus rumen-protected d,l-methionine (MET; 0.9 g/kg dry matter intake). Placentomes collected at term were classified according to cow dietary treatment and offspring sex as follows: Male CON (n = 7), Male MET (n = 7), Female CON (n = 8), and Female MET (n = 8). Calf growth was measured until 9 wk of age. Targeted metabolomics, RT-PCR, global DNA methylation, and activity of selected enzymes in one-carbon metabolism and transsulfuration pathways were performed. Statistics were conducted via ANOVA using MIXED models. Results: At birth, Male MET calves were heavier than Male CON calves (7.6%, P = 0.02), but body mass was similar at 9 wk of age. In contrast, compared with Female CON, Female MET calves had greater body mass at 9 wk of age (6.3%, P = 0.03). Compared with Male CON, placenta from Male MET calves had greater concentrations of tricarboxylic acid (TCA) cycle and transsulfuration intermediates (23-100%, P < 0.05), along with greater 5-methyltetrahydrofolatehomocysteine methyltransferase activity (67%, P = 0.03). Compared with Female CON, placenta from Female MET calves had greater concentrations of one-carbon metabolism intermediates (13-52%, P < 0.05). DNA methyltransferase 3A (DNMT3A) was upregulated (43%, P < 0.01) in placenta from Female MET compared with Female CON calves. Global DNA methylation was lower in placenta from Female MET compared with Female CON calves (45%, P = 0.06). Conclusions: Methionine supply affects placental metabolism, DNA methylation, and body mass of the calf in a sex-specific manner, underscoring its importance as dietary methyl-donor for pregnant cows. PMID: 30608595 [PubMed - as supplied by publisher]

Clinical and genetic analysis of 7 Chinese patients with β-ureidopropionase deficiency.

Sat, 05/01/2019 - 14:54
Related Articles Clinical and genetic analysis of 7 Chinese patients with β-ureidopropionase deficiency. Medicine (Baltimore). 2019 Jan;98(1):e14021 Authors: Fang Y, Cai C, Wang C, Sun B, Zhang X, Fan W, Hu W, Meng Y, Lin S, Zhang C, Zhang Y, Shu J Abstract β-Ureidopropionase (βUP) deficiency is an autosomal recessive disease caused by abnormal changes in the pyrimidine-degradation pathway. This study aimed to investigate the mutation of β-ureidopropionase gene (UPB1) gene and clinical features of 7 Chinese patients with βUP deficiency.We reported 7 Chinese patients with βUP deficiency who were admitted at Tianjin Children's Hospital. Urine metabolomics was detected by gas chromatography-mass spectrometry (GC-MS). Then genetic testing of UPB1 was conducted by polymerase chain reaction (PCR) method.The patients presented with developmental delay, seizures, autism, abnormal magnetic resonance imaging, and significantly elevated levels of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid in urine. Subsequent analysis of UPB1 mutation revealed 2 novel missense mutations (c.851G>T and c.853G>A), 3 previously reported mutations including 2 missense mutations (c.977G>A and c.91G>A) and 1 splice site mutation (c.917-1 G>A).The results suggested that the UPB1 mutation may contribute to βUP deficiency. The c.977G>A is the most common mutation in Chinese population. PMID: 30608453 [PubMed - in process]

Structure annotation of all mass spectra in untargeted metabolomics.

Sat, 05/01/2019 - 14:54
Related Articles Structure annotation of all mass spectra in untargeted metabolomics. Anal Chem. 2019 Jan 04;: Authors: Blaženović I, Kind T, Sa MR, Ji J, Vaniya A, Wancewicz B, Roberts BS, Torbasinovic H, Lee T, Mehta SS, Showalter MR, Song H, Kwok JF, Jahn D, Kim J, Fiehn O Abstract Urine metabolites are used in many clinical and biomedical studies, but usually only for a few classic compounds. Metabolomics detects vastly more metabolic signals that may be used to precisely define the health status of individuals. However, many compounds remain unidentified, hampering biochemical conclusions. Here, we annotate all metabolites detected by two untargeted metabolomic assays, hydrophilic interaction chromatography (HILIC) -Q Exactive HF mass spectrometry and charged surface hybrid (CSH)- Q Exactive HF mass spectrometry. Over 9,000 unique metabolite signals were detected, of which 42% triggered MS/MS fragmentations in data-dependent mode. On the highest Metabolomics Standards Initiative (MSI) confidence level 1, we identified 175 compounds using authentic standards with precursor mass, retention time, and MS/MS matching. Additional 578 compounds were annotated by precursor accurate mass and MS/MS matching alone, MSI level 2, including a novel library specifically geared at acylcarnitines (CarniBlast). The rest of the metabolome is usually left unannotated. To fill this gap, we used the in silico fragmentation tool CSI:FingerID and the new NIST hybrid search to annotate all further compounds (MSI level 3). Testing the top-ranked metabolites in CSI:Finger ID annotations yielded 40% accuracy when applied to the MSI level 1 identified compounds. We classified all MSI level 3 annotations by the NIST hybrid search using the ClassyFire ontology into 21 superclasses that were further distinguished into 184 chemical classes. ClassyFire annotations showed that the previously unannotated urine metabolome consists of 28% derivatives of organic acids, 16% heterocyclics and 16% lipids as major classes. PMID: 30608141 [PubMed - as supplied by publisher]

Metabolomic Biomarkers in Gynecology: a Treasure Path or a False Path?

Sat, 05/01/2019 - 14:54
Related Articles Metabolomic Biomarkers in Gynecology: a Treasure Path or a False Path? Curr Med Chem. 2019 Jan 04;: Authors: Igor G, Stanislav S, Tatyana P, Alexey M, Denis B, Eduard K Abstract Omic-technologies (genomics, transcriptomics, proteomics and metabolomics) have become more important in current medical science. Among them, it is metabolomics that most accurately reflects the minor changes in body functioning, as it focuses on metabolome - the group of the metabolism products, both intermediate and end. Therefore, metabolomics is actively engaged in fundamental and clinical studies and search for potential biomarkers. The biomarker could be used in diagnostics, management and stratification of the patients, as well as in prognosing the outcomes. The good example is gynecology, since many gynecological diseases lack effective biomarkers. In the current review, we aimed to summarize the results of the studies, devoted to the search of potential metabolomic biomarkers for the most common gynecological diseases. PMID: 30608036 [PubMed - as supplied by publisher]

Biomarkers of food intake for Allium vegetables.

Sat, 05/01/2019 - 14:54
Related Articles Biomarkers of food intake for Allium vegetables. Genes Nutr. 2018;13:34 Authors: Praticò G, Gao Q, Manach C, Dragsted LO Abstract Allium vegetables are widely consumed around the world and are known for their potential bioactive components improving human health. These effects have been extensively investigated; however, the results were inconsistent in human studies. Biomarkers of food intake (BFIs) could provide objective measurements of food intake in observational studies and assess compliance in intervention studies. Therefore, the discovery and application of BFIs for Allium vegetables would facilitate the exploring and understanding of the health benefit of Allium vegetables. In this manuscript, we reviewed the currently used and potential candidate BFIs for Allium vegetables and evaluated their levels of validation. S-Allylmercapturic acid (ALMA), allyl methyl sulfide (AMS), allyl methyl sulfoxide (AMSO), allyl methyl sulfone (AMSO2), and S-allylcysteine (SAC), which are derived from organosulfur compounds, were shown to be promising candidate BFIs for garlic consumption. Further validation is needed to assess their robustness and concordance with other measures. Their applicability for the whole food group should be evaluated as well. N-Acetyl-S-(2-carboxypropyl)cysteine (CPMA) was detected in high levels in urine after both garlic and onion intake, suggesting that it may be used for the assessment of intake of Allium food group. The available information regarding its kinetics, robustness, and analytical performance is limited and needs to be assessed in further studies. No candidate BFIs specific to intake of onion, leek, chives, shallots, or ramsons were found. Untargeted metabolomics studies and further validation studies should be performed to discover more reliable BFIs for individual Allium vegetables and the whole food group. This paper serves as an example of Biomarker of Food Intake Reviews (BFIRev) and biomarker of food intake validation procedures. PMID: 30607216 [PubMed]

Continuum of Host-Gut Microbial Co-metabolism: Host CYP3A4/3A7 Are Responsible for Tertiary Oxidations of Deoxycholate Species.

Sat, 05/01/2019 - 14:54
Related Articles Continuum of Host-Gut Microbial Co-metabolism: Host CYP3A4/3A7 Are Responsible for Tertiary Oxidations of Deoxycholate Species. Drug Metab Dispos. 2019 Jan 03;: Authors: Zhang J, Gao LZ, Chen YJ, Zhu PP, Yin SS, Su MM, Ni Y, Miao J, Wu WL, Chen H, Brouwer KLR, Liu CX, Xu L, Jia W, Lan K Abstract The gut microbiota modifies endogenous primary bile acids (BAs) to produce exogenous secondary BAs, which may be further metabolized by cytochrome P450 enzymes (CYPs). Our primary aim was to examine how the host adapts to the stress of microbe-derived secondary BAs by CYPs-mediated oxidative modifications on the steroid nucleus. Five unconjugated tri-hydroxyl BAs that were structurally and/or biologically associated with deoxycholate (DCA) were determined in human biological samples by LC-MS/MS in combination with enzyme-digestion techniques. They were identified as DCA-19-ol, DCA-6β-ol, DCA-5β-ol, DCA-6α-ol, DCA-1β-ol and DCA-4β-ol based on matching with in-lab synthesized standards. Metabolic inhibition assays in human liver microsomes and recombinant CYP assays revealed that CYP3A4 and CYP3A7 were responsible for the regioselective oxidations of both DCA and its conjugated forms, glycodeoxycholate (GDCA) and taurodeoxycholate (TDCA). The modification of secondary BAs to tertiary BAs defines a host liver (primary BAs) - gut microbiota (secondary BAs) - host liver (tertiary BAs) axis. The regioselective oxidations of DCA, GDCA and TDCA by CYP3A4 and CYP3A7 may help eliminate host-toxic DCA species. The 19- and 4β-hydroxylation of DCA species demonstrated outstanding CYP3A7 selectivity and may be useful indicators of CYP3A7 activity. PMID: 30606729 [PubMed - as supplied by publisher]

Urinary Levels of Trimethylamine-N-Oxide and Incident Coronary Heart Disease: A Prospective Investigation Among Urban Chinese Adults.

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Related Articles Urinary Levels of Trimethylamine-N-Oxide and Incident Coronary Heart Disease: A Prospective Investigation Among Urban Chinese Adults. J Am Heart Assoc. 2019 Jan 08;8(1):e010606 Authors: Yu D, Shu XO, Rivera ES, Zhang X, Cai Q, Calcutt MW, Xiang YB, Li H, Gao YT, Wang TJ, Zheng W Abstract Background Trimethylamine-N-oxide ( TMAO ), a diet-derived, gut microbial-host cometabolite, has been associated with adverse cardiovascular outcomes in patient populations; however, evidence is lacking from prospective studies conducted in general populations and non-Western populations. Methods and Results We evaluated urinary levels of TMAO and its precursor metabolites (ie, choline, betaine, and carnitine) in relation to risk of coronary heart disease ( CHD ) among Chinese adults in a nested case-control study, including 275 participants with incident CHD and 275 individually matched controls. We found that urinary TMAO , but not its precursors, was associated with risk of CHD . The odds ratio for the highest versus lowest quartiles of TMAO was 1.91 (95% CI, 1.08-3.35; Ptrend=0.008) after adjusting for CHD risk factors including obesity, diet, lifestyle, and metabolic diseases and 1.75 (95% CI, 0.96-3.18; Ptrend=0.03) after further adjusting for potential confounders or mediators including central obesity, dyslipidemia, inflammation, and intake of seafood and deep-fried meat or fish, which were associated with TMAO level in this study. The odds ratio per standard deviation increase in log- TMAO was 1.30 (95% CI, 1.03-1.63) in the fully adjusted model. A history of diabetes mellitus modified the TMAO - CHD association. A high TMAO level (greater than or equal to versus lower than the median) was associated with odds ratios of 6.21 (95% CI, 1.64-23.6) and 1.56 (95% CI, 1.00-2.43), respectively, among diabetic and nondiabetic participants ( Pinteraction=0.02). Diabetes mellitus status also modified the associations of choline, betaine, and carnitine with risk of CHD ; significant positive associations were found among diabetic participants, but null associations were noted among total and nondiabetic participants. Conclusions Our study suggests that TMAO may accelerate the development of CHD , highlighting the importance of diet-gut microbiota-host interplay in cardiometabolic health. PMID: 30606084 [PubMed - in process]

Diagnostic fragmentation filtering for the discovery of new chaetoglobosins and cytochalasins.

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Related Articles Diagnostic fragmentation filtering for the discovery of new chaetoglobosins and cytochalasins. Rapid Commun Mass Spectrom. 2019 Jan 15;33(1):133-139 Authors: Walsh JP, Renaud JB, Hoogstra S, McMullin DR, Ibrahim A, Visagie CM, Tanney JB, Yeung KK, Sumarah MW Abstract RATIONALE: Microbial natural products are often biosynthesized as classes of structurally related compounds that have similar tandem mass spectrometry (MS/MS) fragmentation patterns. Mining MS/MS datasets for precursor ions that share diagnostic or common features enables entire chemical classes to be identified, including novel derivatives that have previously been unreported. Analytical data analysis tools that can facilitate a class-targeted approach to rapidly dereplicate known compounds and identify structural variants within complex matrices would be useful for the discovery of new natural products. METHODS: A diagnostic fragmentation filtering (DFF) module was developed for MZmine to enable the efficient screening of MS/MS datasets for class-specific product ions(s) and/or neutral loss(es). This approach was applied to series of the structurally related chaetoglobosin and cytochalasin classes of compounds. These were identified from the culture filtrates of three fungal genera: Chaetomium globosum, a putative new species of Penicillium (called here P. cf. discolor: closely related to P. discolor), and Xylaria sp. Extracts were subjected to LC/MS/MS analysis under positive electrospray ionization and operating in a data-dependent acquisition mode, performed using a Thermo Q-Exactive mass spectrometer. All MS/MS datasets were processed using the DFF module and screened for diagnostic product ions at m/z 130.0648 and 185.0704 for chaetoglobosins, and m/z 120.0808 and 146.0598 for cytochalasins. RESULTS: Extracts of C. globosum and P. cf. discolor strains revealed different mixtures of chaetoglobosins, whereas the Xylaria sp. produced only cytochalasins; none of the strains studied produced both classes of compounds. The dominant chaetoglobosins produced by both C. globosum and P. cf. discolor were chaetoglobosins A, C, and F. Tetrahydrochaetoglobosin A was identified from P. cf. discolor extracts and is reported here for the first time as a natural product. The major cytochalasins produced by the Xylaria sp. were cytochalasin D and epoxy cytochalasin D. A larger unknown "cytochalasin-like" molecule with the molecular formula C38 H47 NO10 was detected from Xylaria sp. culture filtrate extracts and is a current target for isolation and structural characterization. CONCLUSIONS: DFF is an effective LC/MS data analysis approach for rapidly identifying entire classes of compounds from complex mixtures. DFF has proved useful in the identification of new natural products and allowing for their partial characterization without the need for isolation. PMID: 30325552 [PubMed - indexed for MEDLINE]

Effects of triphenyl phosphate exposure during fetal development on obesity and metabolic dysfunctions in adult mice: Impaired lipid metabolism and intestinal dysbiosis.

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Related Articles Effects of triphenyl phosphate exposure during fetal development on obesity and metabolic dysfunctions in adult mice: Impaired lipid metabolism and intestinal dysbiosis. Environ Pollut. 2018 Dec 24;246:630-638 Authors: Wang D, Yan S, Yan J, Teng M, Meng Z, Li R, Zhou Z, Zhu W Abstract Previous in vitro studies have implied that triphenyl phosphate (TPHP) may act as an obesogen. However, its specific contributions to the progression of obesity and related metabolic diseases are still unclear in vivo in mice. In this study, we evaluated the effects of in utero and lactational exposure to three doses of TPHP (10, 100, and 1000 μg/kg BW) on obesity and metabolic dysfunctions in adult male mice fed a low-fat diet (LFD) or high-fat diet (HFD), by examining body weight, liver weight, histopathology, blood biochemistry, gene expression, and gut microbiota compositions and metabolic functions. Results showed that TPHP exposure led to increased body weight, liver weight, fat mass, hepatic steatosis, impaired glucose homeostasis, and insulin resistance, and mRNA levels of genes involved in lipid metabolism, especially lipogenesis and lipid accumulation, were significantly altered by TPHP treatment. Gas chromatography-mass spectrometry (GC-MS) analysis further supported the changes in fatty acid composition. Intestinal flora measurements by 16S rRNA gene sequencing and 1H NMR based fecal metabolomics indicated that TPHP treatment modulated gut microbiome composition and influenced host-gut co-metabolism, especially for bile acids and short chain fatty acids (SCFAs). These results suggest that fetal exposure to TPHP can promote the development of obesity and metabolic dysfunctions in adult mice. PMID: 30605818 [PubMed - as supplied by publisher]

Simultaneous isotope dilution quantification and metabolic tracing of deoxyribonucleotides by liquid chromatography high resolution mass spectrometry.

Fri, 04/01/2019 - 14:43
Related Articles Simultaneous isotope dilution quantification and metabolic tracing of deoxyribonucleotides by liquid chromatography high resolution mass spectrometry. Anal Biochem. 2018 Dec 31;: Authors: Kuskovsky R, Buj R, Xu P, Hofbauer S, Doan MT, Jiang H, Bostwick A, Mesaros C, Aird KM, Snyder NW Abstract Quantification of cellular deoxyribonucleoside mono- (dNMP), di- (dNDP), triphosphates (dNTPs) and related nucleoside metabolites are difficult due to their physiochemical properties and widely varying abundance. Involvement of dNTP metabolism in cellular processes including senescence and pathophysiological processes including cancer and viral infection make dNTP metabolism an important bioanalytical target. We modified a previously developed ion pairing reversed phase chromatography-mass spectrometry method for the simultaneous quantification and 13C isotope tracing of dNTP metabolites. dNMPs, dNDPs, and dNTPs were chromatographically resolved to avoid mis-annotation of in-source fragmentation. We used commercially available 13C15N-stable isotope labeled analogs as internal standards and show that this isotope dilution approach improves analytical figures of merit. At sufficiently high mass resolution achievable on an Orbitrap mass analyzer, stable isotope resolved metabolomics allows simultaneous isotope dilution quantification and 13C isotope tracing from major substrates including 13C-glucose. As a proof of principle, we quantified dNMP, dNDP and dNTP pools from multiple cell lines. We also identified isotopologue enrichment from glucose corresponding to ribose from the pentose-phosphate pathway in dNTP metabolites. PMID: 30605633 [PubMed - as supplied by publisher]

METABOLIC PROFILING ANALYSIS UPON ACYLCARNITINES IN TISSUES OF HEPATOCELLULAR CARCINOMA REVEALED THE INHIBITED CARNITINE SHUTTLE SYSTEM CAUSED BY THE DOWNREGULATED CARNITINE PALMITOYLTRANSFERASE 2.

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Related Articles METABOLIC PROFILING ANALYSIS UPON ACYLCARNITINES IN TISSUES OF HEPATOCELLULAR CARCINOMA REVEALED THE INHIBITED CARNITINE SHUTTLE SYSTEM CAUSED BY THE DOWNREGULATED CARNITINE PALMITOYLTRANSFERASE 2. Mol Carcinog. 2019 Jan 03;: Authors: Lu X, Zhang X, Zhang Y, Zhang K, Zhan C, Shi X, Li Y, Zhao J, Bai Y, Wang Y, Nie H, Li Y Abstract The carnitine shuttle system (CSS) plays a crucial role in the transportation of fatty acyls during fatty acid β-oxidation for energy supplementation, especially in cases of high energy demand, such as in cancer. In this study, to systematically characterize alterations of the CSS in hepatocellular carcinoma (HCC), acylcarnitine metabolic profiling was carried out on eighty pairs of HCC tissues and adjacent noncancerous tissues (ANTs) by using ultra-performance liquid chromatography coupled to mass spectrometry. Twenty-four acylcarnitines classified into five categories were identified and characterized between HCCs and ANTs. Notably, increased saturated long-chain acylcarnitines (LCACs) and decreased short- and medium-chain acylcarnitines (S/MCACs) were simultaneously observed in HCC samples. Subsequent correlation network and heatmap analysis indicated low correlations between LCACs and S/MCACs. The mRNA and protein expressions of carnitine palmitoyltransferase 2 (CPT2) was significantly downregulated in HCC samples, whereas CPT1A expression was not significantly changed. Correspondingly, the relative levels of S/MCACs were reduced and those of LCACs were increased in BEL-7402/CPT2-knockdown cells compared to negative controls. Both results suggested that decreased shuttling efficiency in HCC might be associated with downregulation of CPT2. In addition, decreases in the mRNA expression of acetyl-CoA acyltransferase 2 were also observed in HCC tissues and BEL-7402/CPT2-knockdown cells, suggesting potential low β-oxidation efficiency, which was consistent with the increased expression of stearoyl-CoA desaturase 1 in both samples. The systematic strategy applied in our study illustrated decreased shuttling efficiency of the carnitine shuttle system in HCC and can provide biologists with an in-depth understanding of β-oxidation in HCC. This article is protected by copyright. All rights reserved. PMID: 30604893 [PubMed - as supplied by publisher]

Integrated use of LC/MS/MS and LC/Q-TOF/MS targeted metabolomics with automated label-free microscopy for quantification of purine metabolites in cultured mammalian cells.

Fri, 04/01/2019 - 14:43
Related Articles Integrated use of LC/MS/MS and LC/Q-TOF/MS targeted metabolomics with automated label-free microscopy for quantification of purine metabolites in cultured mammalian cells. Purinergic Signal. 2019 Jan 02;: Authors: Nybo SE, Lamberts JT Abstract Purine metabolites have been implicated as clinically relevant biomarkers of worsening or improving Parkinson's disease (PD) progression. However, the identification of purine molecules as biomarkers in PD has largely been determined using non-targeted metabolomics analysis. The primary goal of this study was to develop an economical targeted metabolomics approach for the routine detection of purine molecules in biological samples. Specifically, this project utilized LC/MS/MS and LC/QTOF/MS to accurately quantify levels of six purine molecules in samples from cultured N2a murine neuroblastoma cells. The targeted metabolomics workflow was integrated with automated label-free digital microscopy, which enabled normalization of purine concentration per unit cell in the absence of fluorescent dyes. The established method offered significantly enhanced selectivity compared to previously published procedures. In addition, this study demonstrates that a simple, quantitative targeted metabolomics approach can be developed to identify and quantify purine metabolites in biological samples. We envision that this method could be broadly applicable to quantification of purine metabolites from other complex biological samples, such as cerebrospinal fluid or blood. PMID: 30604179 [PubMed - as supplied by publisher]

Nutritional value of potato (Solanum tuberosum) in hot climates: anthocyanins, carotenoids, and steroidal glycoalkaloids.

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Related Articles Nutritional value of potato (Solanum tuberosum) in hot climates: anthocyanins, carotenoids, and steroidal glycoalkaloids. Planta. 2019 Jan 02;: Authors: Fogelman E, Oren-Shamir M, Hirschberg J, Mandolino G, Parisi B, Ovadia R, Tanami Z, Faigenboim A, Ginzberg I Abstract MAIN CONCLUSION: Growth in hot climates selectively alters potato tuber secondary metabolism-such as the anthocyanins, carotenoids, and glycoalkaloids-changing its nutritive value and the composition of health-promoting components. Potato breeding for improved nutritional value focuses mainly on increasing the health-promoting carotenoids and anthocyanins, and controlling toxic steroidal glycoalkaloids (SGAs). Metabolite levels are genetically determined, but developmental, tissue-specific, and environmental cues affect their final content. Transcriptomic and metabolomic approaches were applied to monitor carotenoid, anthocyanin, and SGA metabolite levels and their biosynthetic genes' expression under heat stress. The studied cultivars differed in tuber flesh carotenoid concentration and peel anthocyanin concentration. Gene expression studies showed heat-induced downregulation of specific genes for SGA, anthocyanin, and carotenoid biosynthesis. KEGG database mapping of the heat transcriptome indicated reduced gene expression for specific metabolic pathways rather than a global heat response. Targeted metabolomics indicated reduced SGA concentration, but anthocyanin pigments concentration remained unchanged, probably due to their stabilization in the vacuole. Total carotenoid level did not change significantly in potato tuber flesh, but their composition did. Results suggest that growth in hot climates selectively alters tuber secondary metabolism, changing its nutritive value and composition of health-promoting components. PMID: 30603793 [PubMed - as supplied by publisher]

Combined use of cutinase and high-resolution mass-spectrometry to query the molecular architecture of cutin.

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Related Articles Combined use of cutinase and high-resolution mass-spectrometry to query the molecular architecture of cutin. Plant Methods. 2018;14:117 Authors: Bhunia RK, Showman LJ, Jose A, Nikolau BJ Abstract Background: Cutin is a complex, highly cross-linked polyester consisting of hydroxylated and epoxidated acyl lipid monomers. Because of the complexity of the polymer it has been difficult to define the chemical architecture of the polymer, which has further limited the ability to identify the catalytic components that assemble the polymer. Analogous to methods that define the structure of oligosaccharides, we demonstrate a strategy that utilizes cutinase to generate cutin subfragments consisting of up to four monomeric units, whose structure and spatial distribution in the polymer is revealed by high-resolution mass spectrometry. Moreover, the application of mass-spectrometric fragmentation and labelling of the end of the oligomers, one is able to define the order of monomers in the oligomer. The systematic application of this strategy can greatly facilitate understanding the chemical architecture of this complex polymer. Results: The chemical architecture of plant cutin is dissected by coupling an enzymatic system that deconstructs the polymer into subfragments consisting of dimers, trimers and tetramers of cutin monomers, with group-specific labeling and mass spectrometry. These subfragments can be generated with one of over 1200 of cutinases identified from diverse biological sources. The parallel chemical labeling of the polymer with dansyl, alkyl or p-dimethylaminophenacyl reagents can identify the chemical distribution of non-esterified hydroxyl- and carboxyl-groups among the monomers. This combined strategy is applied to cutin isolated from with apple fruit skins, and a combination of gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-quadrupole time-of-flight (Q-TOF) MS is used to determine the order of the monomers in the cutinase-generated subfragments. Finally, we demonstrate the use of matrix-assisted laser desorption-ionization-MS to determine the spatial distribution of the cutinase-generated subfragments. Conclusion: Our experimental results demonstrate an advancement to overcome the current limitations in identifying cutin oligomeric structure and allows one to more efficiently address new biological questions about cutin biosynthesis. We submit that the systematic application of these methods will enable the construction of more accurate architectural models of cutin, which is a prerequisite to identifying cutin-biosynthetic components. PMID: 30603042 [PubMed]

Random Forest Analysis of Untargeted Metabolomics Data Suggests Increased Use of Omega Fatty Acid Oxidation Pathway in Drosophila Melanogaster Larvae Fed a Medium Chain Fatty Acid Rich High-Fat Diet.

Fri, 04/01/2019 - 14:43
Related Articles Random Forest Analysis of Untargeted Metabolomics Data Suggests Increased Use of Omega Fatty Acid Oxidation Pathway in Drosophila Melanogaster Larvae Fed a Medium Chain Fatty Acid Rich High-Fat Diet. Metabolites. 2018 Dec 31;9(1): Authors: Oza VH, Aicher JK, Reed LK Abstract Obesity is a complex disease, shaped by both genetic and environmental factors such as diet. In this study, we use untargeted metabolomics and Drosophila melanogaster to model how diet and genotype shape the metabolome of obese phenotypes. We used 16 distinct outbred genotypes of Drosophila larvae raised on normal (ND) and high-fat (HFD) diets, to produce three distinct phenotypic classes; genotypes that stored more triglycerides on a ND relative to the HFD, genotypes that stored more triglycerides on a HFD relative to ND, and genotypes that showed no change in triglyceride storage on either of the two diets. Using untargeted metabolomics we characterized 350 metabolites: 270 with definitive chemical IDs and 80 that were chemically unidentified. Using random forests, we determined metabolites that were important in discriminating between the HFD and ND larvae as well as between the triglyceride phenotypic classes. We found that flies fed on a HFD showed evidence of an increased use of omega fatty acid oxidation pathway, an alternative to the more commonly used beta fatty acid oxidation pathway. Additionally, we observed no correlation between the triglyceride storage phenotype and free fatty acid levels (laurate, caprate, caprylate, caproate), indicating that the distinct metabolic profile of fatty acids in high-fat diet fed Drosophila larvae does not propagate into triglyceride storage differences. However, dipeptides did show moderate differences between the phenotypic classes. We fit Gaussian graphical models (GGMs) of the metabolic profiles for HFD and ND flies to characterize changes in metabolic network structure between the two diets, finding the HFD to have a greater number of edges indicating that metabolome varies more across samples on a HFD. Taken together, these results show that, in the context of obesity, metabolomic profiles under distinct dietary conditions may not be reliable predictors of phenotypic outcomes in a genetically diverse population. PMID: 30602659 [PubMed]

Metabolic response of longitudinal muscles to acute hypoxia in sea cucumber Apostichopus japonicus (Selenka): A metabolome integrated analysis.

Thu, 03/01/2019 - 14:28
Related Articles Metabolic response of longitudinal muscles to acute hypoxia in sea cucumber Apostichopus japonicus (Selenka): A metabolome integrated analysis. Comp Biochem Physiol Part D Genomics Proteomics. 2018 Dec 27;29:235-244 Authors: Li L, Chen M, Storey KB Abstract Hypoxia is a severe problem in aquatic environments worldwide and has caused mass mortality of sea cucumbers (& other species) for decades, seriously affecting the sustainable development of aquaculture. Investigations of the metabolic disruptions and biochemical responses associated with acute hypoxia stress in sea cucumbers can provide a theoretical basis and guidance for improving aquaculture. A metabolomics approach to characterize changes in the profiles of endogenous small molecules in response to acute hypoxia can help to identify the main underlying causes of metabolic damage and potentially suggest solutions to alleviate to improve viability. The current study uses liquid chromatography-mass spectrometry (LC-MS) and multivariate analysis methods to evaluate the metabolic profile of longitudinal muscles from A. japonicus exposed to acute hypoxia stress (by bubbling the aquaria water with nitrogen aeration to decrease dissolved oxygen to 2 mg/L in 2 min) for 6 or 24 h (experimental groups EG6 or EG24) and control group (CG, n = 10, respectively). The results showed that 29 and 62 metabolites were influenced significantly in EG6 and EG24, respectively, mainly including lipids, glycosides and their derivatives. Levels of most lipids (fatty acids, glycerolipids, glycerophospholipids, sphingolipids and sterols) were elevated in both experimental groups, and increased with elongation of hypoxia, implying that the homeostasis of synthesis and degradation of lipids and their derivatives was strongly affected by hypoxia stress. Pathway enrichment analysis was performed to further assess the importance of differential metabolite expression to the development of the A. japonicus response to hypoxia, showing that 4 (fatty acid biosynthesis, d-glutamine and d-glutamate metabolism, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate metabolism) and 2 (steroid biosynthesis, longevity regulating pathway) pathways were markedly enriched in EG6 and EG24, respectively. These results suggested that fatty acid synthesis was strengthened significantly in both treatment groups, and the degree was higher in EG24 than in EG6, providing valuable information towards understanding the special adaptive mechanism of A. japonicus to hypoxia stress. PMID: 30602139 [PubMed - as supplied by publisher]

Large-scale profiling of serum metabolites in African American and European American patients with bladder cancer reveals metabolic pathways associated with patient survival.

Thu, 03/01/2019 - 14:28
Related Articles Large-scale profiling of serum metabolites in African American and European American patients with bladder cancer reveals metabolic pathways associated with patient survival. Cancer. 2019 Jan 02;: Authors: Vantaku V, Donepudi SR, Piyarathna DWB, Sekhar Amara C, Ambati CR, Tang W, Putluri V, Chandrashekar DS, Varambally S, Terris MK, Davies K, Ambs S, Bollag R, Apolo AB, Sreekumar A, Putluri N Abstract BACKGROUND: African Americans (AAs) experience a disproportionally high rate of bladder cancer (BLCA) deaths even though their incidence rates are lower than those of other patient groups. Using a metabolomics approach, this study investigated how AA BLCA may differ molecularly from European Americans (EAs) BLCA, and it examined serum samples from patients with BLCA with the aim of identifying druggable metabolic pathways in AA patients. METHODS: Targeted metabolomics was applied to measure more than 300 metabolites in serum samples from 2 independent cohorts of EA and AA patients with BLCA and healthy EA and AA controls via liquid chromatography-mass spectrometry, and this was followed by the identification of altered metabolic pathways with a focus on AA BLCA. A subset of the differential metabolites was validated via absolute quantification with the Biocrates AbsoluteIDQ p180 kit. The clinical significance of the findings was further examined in The Cancer Genomic Atlas BLCA data set. RESULTS: Fifty-three metabolites, mainly related to amino acid, lipid, and nucleotide metabolism, were identified that showed significant differences in abundance between AA and EA BLCA. For example, the levels of taurine, glutamine, glutamate, aspartate, and serine were elevated in serum samples from AA patients versus EA patients. By mapping these metabolites to genes, this study identified significant relations with regulators of metabolism such as malic enzyme 3, prolyl 3-hydroxylase 2, and lysine demethylase 2A that predicted patient survival exclusively in AA patients with BLCA. CONCLUSIONS: This metabolic profile of serum samples might be used to assess risk progression in AA BLCA. These first-in-field findings describe metabolic alterations in AA BLCA and emphasize a potential biological basis for BLCA health disparities. PMID: 30602056 [PubMed - as supplied by publisher]

MetFlow: An interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery.

Thu, 03/01/2019 - 14:28
Related Articles MetFlow: An interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery. Bioinformatics. 2019 Jan 02;: Authors: Shen X, Zhu ZJ Abstract Summary: Mass spectrometry-based metabolomics aims to profile the metabolic changes in biological systems and identify differential metabolites related to physiological phenotypes and aberrant activities. However, many confounding factors during data acquisition complicate metabolomics data, which is characterized by high dimensionality, uncertain degrees of missing and zero values, nonlinearity, unwanted variations, and non-normality. Therefore, prior to differential metabolite discovery analysis, various types of data cleaning such as batch alignment, missing value imputation, data normalization, and scaling are essentially required for data post-processing. Here, we developed an interactive web server, namely, MetFlow, to provide an integrated and comprehensive workflow for metabolomics data cleaning and differential metabolite discovery. Availability and implementation: The MetFlow is freely available on http://metflow.zhulab.cn/. Supplementary information: Supplementary data are available at Bioinformatics online. PMID: 30601938 [PubMed - as supplied by publisher]

Obesity Leads to Distinct Metabolomic Signatures in the Follicular Fluid of Women Undergoing in vitro Fertilization.

Thu, 03/01/2019 - 14:28
Related Articles Obesity Leads to Distinct Metabolomic Signatures in the Follicular Fluid of Women Undergoing in vitro Fertilization. Am J Physiol Endocrinol Metab. 2019 Jan 02;: Authors: Ruebel ML, Piccolo BD, Mercer KE, Pack L, Moutos D, Shankar K, Andres A Abstract While obesity negatively influences the metabolic homeostasis of cells within a broad range of tissues, its impact on oocyte metabolism is not fully understood. Prior evidence suggests obesity increases expression of oocyte genes associated with inflammation, oxidative stress, and lipid metabolism; however, the metabolic impact of these genetic differences is not known. To address this gap, we conducted an exploratory assessment of the follicular fluid (FF) metabolome in 8 overweight/obese (OW) and 9 normal weight (NW) women undergoing in vitro fertilization. FF and serum were collected and analyzed by untargeted metabolomics using GC-QTOF-MS and CSH-ESI QTOF MS/MS. Untargeted metabolomics identified obesity-associated changes in FF metabolites related to oxidative stress/antioxidant capacity, xenometabolism/amino acid biosynthesis, and lipid metabolism. Discriminant FF metabolites included elevated uric acid, isothreonic acid, 1 unknown primary metabolite, and 6 unknown complex lipids in OW compared to NW women. Conversely, 2-dimethylacetal-ketoglucose, aminomalonate, 2 unknown primary metabolites, and 2 unknown complex lipids were decreased in FF of OW relative to NW women. Indole-3-propionic acid (IPA), a bacterial derived metabolite, was also decreased in both FF and serum of OW women (p<0.05). The significant correlation between antioxidant IPA in serum and FF (R= 0.95, p<0.0001), suggests a potential serum biomarker of FF antioxidant status or reflection of the gut metabolism interaction with the follicle. These results suggest that obesity has important consequences on the follicular environment during the pre-conception period, a window of time that may be important for lifestyle interventions to ameliorate obesity-associated risk factors. PMID: 30601701 [PubMed - as supplied by publisher]

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