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: 2 hours 55 min ago

Aspartylglycosamine is a biomarker for NGLY1-CDDG, a congenital disorder of deglycosylation.

Thu, 18/07/2019 - 12:02
Aspartylglycosamine is a biomarker for NGLY1-CDDG, a congenital disorder of deglycosylation. Mol Genet Metab. 2019 Jul 09;: Authors: Haijes HA, de Sain-van der Velden MGM, Prinsen HCMT, Willems AP, van der Ham M, Gerrits J, Couse MH, Friedman JM, van Karnebeek CDM, Selby KA, van Hasselt PM, Verhoeven-Duif NM, Jans JJM Abstract BACKGROUND: NGLY1-CDDG is a congenital disorder of deglycosylation caused by a defective peptide:N-glycanase (PNG). To date, all but one of the reported patients have been diagnosed through whole-exome or whole-genome sequencing, as no biochemical marker was available to identify this disease in patients. Recently, a potential urinary biomarker was reported, but the data presented suggest that this marker may be excreted intermittently. METHODS: In this study, we performed untargeted direct-infusion high-resolution mass spectrometry metabolomics in seven dried blood spots (DBS) from four recently diagnosed NGLY1-CDDG patients, to test for small-molecule biomarkers, in order to identify a potential diagnostic marker. Results were compared to 125 DBS of healthy controls and to 238 DBS of patients with other diseases. RESULTS: We identified aspartylglycosamine as the only significantly increased compound with a median Z-score of 4.8 (range: 3.8-8.5) in DBS of NGLY1-CDDG patients, compared to a median Z-score of -0.1 (range: -2.1-4.0) in DBS of healthy controls and patients with other diseases. DISCUSSION: The increase of aspartylglycosamine can be explained by lack of function of PNG. PNG catalyzes the cleavage of the proximal N-acetylglucosamine residue of an N-glycan from the asparagine residue of a protein, a step in the degradation of misfolded glycoproteins. PNG deficiency results in a single N-acetylglucosamine residue left attached to the asparagine residue which results in free aspartylglycosamine when the glycoprotein is degraded. Thus, we here identified aspartylglycosamine as the first potential small-molecule biomarker in DBS for NGLY1-CDDG, making a biochemical diagnosis for NGLY1-CDDG potentially feasible. PMID: 31311714 [PubMed - as supplied by publisher]

Red carotenoids and associated gene expression explain colour variation in frillneck lizards.

Thu, 18/07/2019 - 12:02
Red carotenoids and associated gene expression explain colour variation in frillneck lizards. Proc Biol Sci. 2019 Jul 24;286(1907):20191172 Authors: McLean CA, Lutz A, Rankin KJ, Elliott A, Moussalli A, Stuart-Fox D Abstract A long-standing hypothesis in evolutionary ecology is that red-orange ornamental colours reliably signal individual quality owing to limited dietary availability of carotenoids and metabolic costs associated with their production, such as the bioconversion of dietary yellow carotenoids to red ketocarotenoids. However, in ectothermic vertebrates, these colours can also be produced by self-synthesized pteridine pigments. As a consequence, the relative ratio of pigment types and their biochemical and genetic basis have implications for the costs and information content of colour signals; yet they remain poorly known in most taxonomic groups. We tested whether red- and yellow-frilled populations of the frillneck lizard, Chlamydosaurus kingii, differ in the ratio of different biochemical classes of carotenoid and pteridine pigments, and examined associated differences in gene expression. We found that, unlike other squamate reptiles, red hues derive from a higher proportion of ketocarotenoids relative to both dietary yellow carotenoids and to pteridines. Whereas red frill skin showed higher expression of several genes associated with carotenoid metabolism, yellow frill skin showed higher expression of genes associated with steroid hormones. Based on the different mechanisms underlying red and yellow signals, we hypothesize that frill colour conveys different information in the two populations. More generally, the data expand our knowledge of the genetic and biochemical basis of colour signals in vertebrates. PMID: 31311479 [PubMed - in process]

Taste Evaluation of Yellowtail (Seriola Quinqueradiata) Ordinary and Dark Muscle by Metabolic Profiling.

Thu, 18/07/2019 - 12:02
Taste Evaluation of Yellowtail (Seriola Quinqueradiata) Ordinary and Dark Muscle by Metabolic Profiling. Molecules. 2019 Jul 15;24(14): Authors: Mabuchi R, Ishimaru A, Adachi M, Zhao H, Kikutani H, Tanimoto S Abstract We performed metabolic profiling on yellowtail (Seriola quinqueradiata) muscle to develop an objective taste evaluation method for fish meat. Dark (DM) and ordinary (OM) muscle samples before and after storage were subjected to gas chromatography-mass spectrometry (GC-MS) analysis and taste measurements using an electronic tongue. The metabolites identified by the GC-MS analysis were treated as x variables, and the taste values obtained by the electronic tongue were treated as y variables. The relationships between the metabolites and taste attributes were evaluated by two-way orthogonal projections to latent structures (O2PLS) analysis. The O2PLS analyses were normalized in two ways, unit variance (UV) and pareto (Par) scaling. The O2PLS (UV) analysis produced 3+1+0 models in Autofit and this model was statistically significant with R2Y (0.73) and Q2 (0.52) metrics. In particular, significant correlations were found between DM or OM and metabolite intensity and taste attributes, and strong associations were found between "sourness" and lysine, "irritant" and alanine and phenylalanine, "saltiness" and pantothenic acid, and "umami" and creatinine and histidine. The O2PLS (Par) analysis of DM generated significant predictive models for "acidic bitterness," "irritant," "saltiness," "bitterness," "astringency," and "richness." Among these, only "irritant" was affected by storage. This method was thus effective in evaluating the taste of yellowtail muscle. PMID: 31311195 [PubMed - in process]

Non-targeted Metabolomic Analysis Based on Ultra-High-Performance Liquid Chromatography Quadrupole Time-of-Flight Tandem Mass Spectrometry Reveals the Effects of Grafting on Non-volatile Metabolites in Fresh Tea Leaves ( Camellia sinensis L.).

Thu, 18/07/2019 - 12:02
Related Articles Non-targeted Metabolomic Analysis Based on Ultra-High-Performance Liquid Chromatography Quadrupole Time-of-Flight Tandem Mass Spectrometry Reveals the Effects of Grafting on Non-volatile Metabolites in Fresh Tea Leaves ( Camellia sinensis L.). J Agric Food Chem. 2019 Jun 12;67(23):6672-6682 Authors: Qi D, Li J, Qiao X, Lu M, Chen W, Miao A, Guo W, Ma C Abstract To investigate the effects of grafting on non-volatile metabolites in tea, non-targeted metabolomic analyses of fresh leaves were performed on the basis of ultra-high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF/MS). One non-grafted YingHong No. 9 and four grafted tea [grafting scion YingHong No. 9 on four different rootstocks, BaiMao No. 2 (BM2), BaiYeDanCong (BY), HeiYeShuiXian (HY), and WuLingHong (WLH)] were chosen as materials. In total, 32 differential metabolites were identified, including phenolic acids, flavan-3-ols, dimeric catechins, flavonol and flavonol/flavone glycosides, etc. Partial least squares discrimination analysis and hierarchical cluster analysis showed various effects of different rootstocks on metabolites. Thereinto, rootstocks of WLH and BY showed extremely outstanding performance in up- and downregulating these metabolites, respectively. Differential metabolites were enriched into three crucial pathways, including biosynthesis of phenylpropanoids, flavonoid biosynthesis, and flavone and flavonol biosynthesis, which might influence the quality of tea. This study provides a theoretical basis for grafting-related variations of non-volatile metabolites in fresh tea leaves. PMID: 31117493 [PubMed - indexed for MEDLINE]

metabolomics; +19 new citations

Wed, 17/07/2019 - 14:49
19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/07/17PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +27 new citations

Tue, 16/07/2019 - 14:39
27 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/07/16PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Ilexgenin A prevents early colonic carcinogenesis and reprogramed lipid metabolism through HIF1α/SREBP-1.

Sun, 14/07/2019 - 14:13
Ilexgenin A prevents early colonic carcinogenesis and reprogramed lipid metabolism through HIF1α/SREBP-1. Phytomedicine. 2019 Jul 02;63:153011 Authors: Zhang L, Qiao X, Chen M, Li P, Wen X, Sun M, Ma X, Hou Y, Yang J Abstract BACKGROUND: Ilexgenin A (IA), the main bioactive compound from Ilex hainanensis Merr., has significant hypolipidemic activities. However, the effects of IA on colitis-associated colorectal cancer (CRC) and its mechanisms are still unknown. PURPOSE: The study was designed to evaluate the effect of IA on CRC and explore its underlying mechanisms. STUDY DESIGN: The effect of IA on colitis related CRC were evaluated in azoxymethane (AOM)/dextran sulfate sodium (DSS) mice and the underlying mechanisms were revealed by metabolomics, which were further validated in vivo and in vitro. METHODS: The Balb/c mice were treated with AOM/DSS to induce CRC model and fed with normal diet with or without 0.02% IA. After the experimental period, samples of plasma were collected and analyzed by ultra-high-performance liquid chromatography/quadrupole time off light mass spectrometry (UHPLC-Q-TOF). Multivariate statistical tools were used to identify the changes of serum metabolites associated with CRC and responses to IA treatment. HT 29 and HCT 116 cells were stimulated by palmitate (PA) and cultured under hypoxia. Western blot, Q-PCR, and Immunofluorescence staining were performed to confirm the molecular pathway in vivo and in vitro. RESULTS: Our results showed IA significantly inhibited the inflammatory colitis symptoms such as disease activity index score, shortening of colon tissues and the increase of inflammatory cytokines. In metabolomic study, 31 potential metabolites associated with CRC were identified and 24 of them were reversed by IA treatment. Most of biomarkers were associated with arachidonic acid metabolism, glycerophospholipid catabolism, and phospholipid metabolism, suggesting lipid metabolism might be involved in the beneficial effect of IA on CRC. Furthermore, we also found IA could decrease the expressions of SREBP-1 and its target gene in the colon tissues of AOM/DSS mice. It could down-regulate the triglyceride (TG) content and the expressions of HIF1α, SREBP-1, FASN, and ACC in HT 29 and HCT 116 cells. The inhibitory effect of IA on SREBP-1 was also attenuated by desferrioxamine (DFX), suggesting HIF1α is involved in the regulation of IA on SREBP-1. CONCLUSION: IA prevents early colonic carcinogenesis in AOM/DSS mice and reprogramed lipid metabolism partly through HIF1α/SREBP-1. PMID: 31301538 [PubMed - as supplied by publisher]

Effects of Fecal Microbiota Transplantation With Oral Capsules in Obese Patients.

Sun, 14/07/2019 - 14:13
Effects of Fecal Microbiota Transplantation With Oral Capsules in Obese Patients. Clin Gastroenterol Hepatol. 2019 Jul 10;: Authors: Allegretti JR, Kassam Z, Mullish BH, Chiang A, Carrellas M, Hurtado J, Marchesi JR, McDonald JAK, Pechlivanis A, Barker GF, Blanco JM, Garcia-Perez I, Wong WF, Gerardin Y, Silverstein M, Kennedy K, Thompson C Abstract BACKGROUND & AIMS: Studies in mice have shown that the intestinal microbiota can contribute to obesity via the anorexigenic gut hormone glucagon-like peptide 1 (GLP1) and bile acids, which affect lipid metabolism. We performed a randomized, placebo-controlled pilot study of the effects of fecal microbiota transplantation (FMT) in obese, metabolically uncompromised patients. METHODS: We performed a double-blind study of 22 obese patients (body mass index [BMI] ≥ 35kg/m2) without a diagnosis of diabetes, non-alcoholic steatohepatitis, or metabolic syndrome. Participants were randomly assigned (1:1) to groups that received FMT by capsules (induction dose of 30 capsules at week 4 and maintenance dose of 12 capsules at week 8) or placebo capsules. FMT capsules were derived from a single, lean donor (BMI, 17.5 kg/m2). Patients were followed through week 26; the primary outcome was safety. Stool and serum samples were collected from patients at baseline and at weeks 1, 4, 6, 8 and 12 after administration of the first dose of FMT or placebo and analyzed by 16S RNA gene sequencing. Stool and serum samples were analyzed for metabolomics by liquid chromatography-mass spectrometry. Additional outcomes were change in area under the curve for GLP1 at week 12. RESULTS: We observed no significant differences in adverse events between patients who received FMT vs placebo. There was no increase in the area under the curve of GLP1 in either group. Patients who received FMT had sustained shifts in microbiomes associated with obesity toward those of the donor (P<.001). Patients who received FMT had a sustained decrease in stool levels of taurocholic acid (P<.05), compared with baseline; bile acid profiles began to more closely resemble those of the donor. We did not observe significant changes in mean BMI at week 12 in either group. CONCLUSIONS: In a placebo-controlled pilot study, we found that FMT capsules (derived from a lean donor) were safe but did not reduce BMI in obese metabolically uncompromised patients. The FMT capsules were well tolerated and led to sustained changes in the intestinal microbiome and bile acid profiles that were similar to those of the lean donor. PMID: 31301451 [PubMed - as supplied by publisher]

Identification ofendogenous small peptides involved in rice immunity through transcriptomics- and proteomics-based screening.

Sun, 14/07/2019 - 14:13
Identification ofendogenous small peptides involved in rice immunity through transcriptomics- and proteomics-based screening. Plant Biotechnol J. 2019 Jul 13;: Authors: Wang P, Yao S, Kosami KI, Guo T, Li J, Zhang Y, Fukao Y, Kaneko-Kawano T, Zhang H, She YM, Wang P, Xing W, Hanada K, Liu R, Kawano Y Abstract Small signaling peptides, generated from larger protein precursors, are important components to orchestrate various plant processes such as development and immune responses. However, small signaling peptides involved in plant immunity remain largely unknown. Here, we developed a pipeline using transcriptomicsand proteomics-based screening to identify putative precursors of small signaling peptides:small secreted proteins (SSPs) in rice, induced by rice blast fungus Magnaportheoryzaeand its elicitor, chitin. We identified 236 SSPs including members of two known small signalingpeptide familiesnamely rapid alkalinization factors and phytosulfokines, as well as many other protein families that are known to be involved in immunity, such as proteinase inhibitors and pathogenesis-related protein families. We also isolated 52 unannotated SSPs, and among them, we found one gene which we namedimmune response peptide(IRP)that appeared to encode the precursor of a small signalingpeptide regulating rice immunity. In rice suspension cells, the expression of IRPwas induced by bacterial peptidoglycan andfungal chitin.Overexpression of IRP enhanced the expression of adefence gene, PAL1and induced the activation of the MAPKs inrice cells. Moreover, the IRP protein level increased insuspension cell medium after chitin treatment. Collectively, we established a simple and efficient pipelineto discover SSPcandidates that may play important roles in rice immunity, and identified 52 unannotated SSPs that may be useful for further elucidation of rice immunity. Our method may be applied to identify SSPs that are involved not only in immunity but also in other plant functions. This article is protected by copyright. All rights reserved. PMID: 31301098 [PubMed - as supplied by publisher]

Metabolomics Differential Analysis Reveals Clinostat Rotation Affects Metabolite Transportation and Increases Organic Acid Production of Aspergillus carbonarius.

Sun, 14/07/2019 - 14:13
Metabolomics Differential Analysis Reveals Clinostat Rotation Affects Metabolite Transportation and Increases Organic Acid Production of Aspergillus carbonarius. Appl Environ Microbiol. 2019 Jul 12;: Authors: Jiang C, Guo D, Li Z, Lei S, Shi J, Shao D Abstract Contamination by fungi may pose a threat to the long-term operation of the space station because fungi produce organic acids that corrode equipment and mycotoxins that harm human health. Microgravity is an unavoidable and special condition in the space station. However, the influence of microgravity on fungal metabolism has not been well studied. Clinostat rotation is widely used to simulate the microgravity condition in studies carried out on Earth. Here, we used metabolomics differential analysis to study the influence of clinostat rotation on the accumulation of organic acids and related biosynthetic pathways in ochratoxin A (OTA)-producing Aspergillus carbonarius As results, clinostat rotation did not affect fungal cell growth or colony appearance, but significantly increased the accumulation of organic acids and OTA both inside cells and in the medium, particularly isocitric acid, citric acid, oxalic acid, as well as a much higher accumulation of some products inside than outside cells, indicating that transport of these metabolites from the cell to the medium was inhibited. This finding corresponded with the change in fatty acid composition of cell membranes and reduced thickness of the cell walls and cell membranes. Amino acid and energy metabolic pathways, particularly the TCA cycle was influenced the most during clinostat rotation compared to normal gravity.IMPORTANCEFungi are ubiquitous in nature and have the ability to corrode various materials by producing metabolites. Research on how the space station environment, especially microgravity, affects fungal metabolism is helpful to understand the role of fungi in space station. This work provides insights on the mechanisms involved in metabolism of corrosive fungus Aspergillus carbonarius under simulated microgravity condition. Our findings have significance not only for preventing material corrosion, but also for ensuring food safety, especially in the space environment. PMID: 31300399 [PubMed - as supplied by publisher]

metabolomics; +23 new citations

Sat, 13/07/2019 - 13:57
23 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/07/13PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +17 new citations

Fri, 12/07/2019 - 19:54
17 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/07/12PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Plasma Metabolites Associated with Frequent Red Wine Consumption: A Metabolomics Approach within the PREDIMED Study.

Thu, 11/07/2019 - 22:40
Plasma Metabolites Associated with Frequent Red Wine Consumption: A Metabolomics Approach within the PREDIMED Study. Mol Nutr Food Res. 2019 Jul 10;:e1900140 Authors: Hernández-Alonso P, Papandreou C, Bulló M, Ruiz-Canela M, Dennis C, Deik A, Wang DD, Guasch-Ferré M, Yu E, Toledo E, Razquin C, Corella D, Estruch R, Ros E, Fitó M, Arós F, Fiol M, Serra-Majem L, Liang L, Clish CB, Martínez-González MA, Hu FB, Salas-Salvadó J Abstract SCOPE: The relationship between red wine (RW) consumption and metabolism is poorly understood. We aimed to assess the systemic metabolomic profiles in relation to frequent RW consumption as well as the ability of a set of metabolites to discriminate RW consumers. METHODS AND RESULTS: Cross-sectional analysis of 1,157 participants. Subjects were divided as non-RW consumers versus RW consumers (> 1 glass/day RW (100 mL/day)). Plasma metabolomics analysis was performed using LC-MS. Associations between 386 identified metabolites and RW consumption were assessed using elastic net regression analysis taking into consideration baseline significant covariates. Ten-cross-validation (CV) was performed and receiver operating characteristic curves were constructed in each of the validation datasets based on weighted models. A subset of 13 metabolites was consistently selected and discriminated RW consumers versus non-consumers. Based on the multi-metabolite model weighted with the regression coefficients of metabolites, the area under the curve was 0.83 (95% CI: 0.80-0.86). These metabolites mainly consisted of lipid species (e.g. triglycerides and phosphatidylcholines), some organic acids and alkaloids. CONCLUSIONS: A multi-metabolite model identified in a Mediterranean population appeared useful to discriminate between frequent RW consumers and non-consumers. Further studies are needed to assess the contribution of these metabolites in health and disease. This article is protected by copyright. All rights reserved. PMID: 31291050 [PubMed - as supplied by publisher]

Deep Metabolomics of a High-Grade Serous Ovarian Cancer Triple-Knockout Mouse Model.

Thu, 11/07/2019 - 22:40
Deep Metabolomics of a High-Grade Serous Ovarian Cancer Triple-Knockout Mouse Model. J Proteome Res. 2019 Jul 10;: Authors: Huang D, Gaul DA, Nan H, Kim J, Fernández FM Abstract High-grade serous carcinoma (HGSC) is the most common and deadliest ovarian cancer (OC) type, accounting for 70-80% of OC deaths. This high mortality is largely due to late diagnosis. Early detection is thus crucial to reduce mortality, yet the tumor pathogenesis of HGSC remains poorly understood, making early detection exceedingly difficult. Faithfully and reliably representing the clinical nature of human HGSC, a recently developed triple-knockout (TKO) mouse model offers a unique opportunity to examine the entire disease spectrum of HGSC. Metabolic alterations were investigated by applying ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) to serum samples collected from these mice at premalignant, early, and advanced stages of HGSC. This comprehensive analysis revealed a panel of 29 serum metabolites that distinguished mice with HGSC from controls and mice with uterine tumors with over 95% accuracy. Meanwhile, our panel could further distinguish early-stage HGSC from controls with 100% accuracy and from advanced-stage HGSC with over 90% accuracy. Important identified metabolites included phospholipids, sphingomyelins, sterols, N-acyltaurine, oligopeptides, bilirubin, 2(3)-hydroxysebacic acids, uridine, N-acetylneuraminic acid, and pyrazine derivatives. Overall, our study provides insights into dysregulated metabolism associated with HGSC development and progression, and serves as a useful guide toward early detection. PMID: 31290664 [PubMed - as supplied by publisher]

A large-scale analysis of targeted metabolomics data from heterogeneous biological samples provides insights into metabolite dynamics.

Thu, 11/07/2019 - 22:40
A large-scale analysis of targeted metabolomics data from heterogeneous biological samples provides insights into metabolite dynamics. Metabolomics. 2019 Jul 09;15(7):103 Authors: Lee HJ, Kremer DM, Sajjakulnukit P, Zhang L, Lyssiotis CA Abstract INTRODUCTION: We previously developed a tandem mass spectrometry-based label-free targeted metabolomics analysis framework coupled to two distinct chromatographic methods, reversed-phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC), with dynamic multiple reaction monitoring (dMRM) for simultaneous detection of over 200 metabolites to study core metabolic pathways. OBJECTIVES: We aim to analyze a large-scale heterogeneous data compendium generated from our LC-MS/MS platform with both RPLC and HILIC methods to systematically assess measurement quality in biological replicate groups and to investigate metabolite abundance changes and patterns across different biological conditions. METHODS: Our metabolomics framework was applied in a wide range of experimental systems including cancer cell lines, tumors, extracellular media, primary cells, immune cells, organoids, organs (e.g. pancreata), tissues, and sera from human and mice. We also developed computational and statistical analysis pipelines, which include hierarchical clustering, replicate-group CV analysis, correlation analysis, and case-control paired analysis. RESULTS: We generated a compendium of 42 heterogeneous deidentified datasets with 635 samples using both RPLC and HILIC methods. There exist metabolite signatures that correspond to various phenotypes of the heterogeneous datasets, involved in several metabolic pathways. The RPLC method shows overall better reproducibility than the HILIC method for most metabolites including polar amino acids. Correlation analysis reveals high confidence metabolites irrespective of experimental systems such as methionine, phenylalanine, and taurine. We also identify homocystine, reduced glutathione, and phosphoenolpyruvic acid as highly dynamic metabolites across all case-control paired samples. CONCLUSIONS: Our study is expected to serve as a resource and a reference point for a systematic analysis of label-free LC-MS/MS targeted metabolomics data in both RPLC and HILIC methods with dMRM. PMID: 31289941 [PubMed - in process]

Insights into Allosteric Control of Human Blood Group A and B Glycosyltransferases from Dynamic NMR.

Thu, 11/07/2019 - 22:40
Insights into Allosteric Control of Human Blood Group A and B Glycosyltransferases from Dynamic NMR. ChemistryOpen. 2019 Jun;8(6):760-769 Authors: Flügge F, Peters T Abstract Human blood group A and B glycosyltransferases (GTA, GTB) are retaining glycosyltransferases, requiring a catalytic mechanism that conserves the anomeric configuration of the hexopyranose moiety of the donor substrate (UDP-GalNAc, UDP-Gal). Previous studies have shown that GTA and GTB cycle through structurally distinct states during catalysis. Here, we link binding and release of substrates, substrate-analogs, and products to transitions between open, semi-closed, and closed states of the enzymes. Methyl TROSY based titration experiments in combination with zz-exchange experiments uncover dramatic changes of binding kinetics associated with allosteric interactions between donor-type and acceptor-type ligands. Taken together, this highlights how allosteric control of on- and off-rates correlates with conformational changes, driving catalysis to completion. PMID: 31289712 [PubMed]

Global serum metabolomics profiling of colorectal cancer.

Thu, 11/07/2019 - 22:40
Global serum metabolomics profiling of colorectal cancer. Mol Clin Oncol. 2019 Jul;11(1):3-14 Authors: Hashim NAA, Ab-Rahim S, Suddin LS, Saman MSA, Mazlan M Abstract Accurate diagnosis of colorectal cancer (CRC) relies on the use of invasive tools such as colonoscopy and sigmoidoscopy. Non-invasive tools are less sensitive in detecting the disease, particularly in the early stage. A number of researchers have used metabolomics analyses on serum/plasma samples of patients with CRC compared with normal healthy individuals in an effort to identify biomarkers for CRC. The aim of the present review is to compare reported serum metabolomics profiles of CRC and to identify common metabolites affected among these studies. A literature search was performed to include any experimental studies on global metabolomics profile of CRC using serum/plasma samples published up to March 2018. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool was used to assess the quality of the studies reviewed. In total, nine studies were included. The studies used various analytical platforms and were performed on different populations. A pathway enrichment analysis was performed using the data from all the studies under review. The most affected pathways identified were protein biosynthesis, urea cycle, ammonia recycling, alanine metabolism, glutathione metabolism and citric acid cycle. The metabolomics analysis revealed levels of metabolites of glycolysis, tricarboxylic acid cycle, anaerobic respiration, protein, lipid and glutathione metabolism were significantly different between cancer and control samples. Although the majority of differentiating metabolites identified were different in the different studies, there were several metabolites that were common. These metabolites include pyruvic acid, glucose, lactic acid, malic acid, fumaric acid, 3-hydroxybutyric acid, tryptophan, phenylalanine, tyrosine, creatinine and ornithine. The consistent dysregulation of these metabolites among the different studies suggest the possibility of common diagnostic biomarkers for CRC. PMID: 31289671 [PubMed]

Ectopic defense gene expression is associated with growth defects in Medicago truncatula lignin pathway mutants.

Thu, 11/07/2019 - 22:40
Ectopic defense gene expression is associated with growth defects in Medicago truncatula lignin pathway mutants. Plant Physiol. 2019 Jul 09;: Authors: Ha CM, Fine D, Bhatia A, Rao X, Martin M, Engle N, Wherritt DJ, Tschaplinski T, Sumner L, Dixon RA Abstract Lignin provides essential mechanical support for plant cell walls but decreases the digestibility of forage crops and increases the recalcitrance of biofuel crops. Attempts to modify lignin content and/or composition by genetic modification often result in negative growth effects. Although several studies have attempted to address the basis for such effects in individual transgenic lines, no common mechanism linking lignin modification with perturbations in plant growth and development has yet been identified. To address whether a common mechanism exists, we have analyzed transposon insertion mutants resulting in independent loss of function of five enzymes of the monolignol pathway, as well as one double mutant, in the model legume Medicago truncatula. These plants exhibit growth phenotypes from essentially wild-type to severely retarded. Extensive phenotypic, transcriptomic, and metabolomics analyses, including structural characterization of differentially expressed compounds, revealed diverse phenotypic consequences of lignin pathway perturbation that were perceived early in plant development, but were not predicted by lignin content or composition alone. Notable phenotypes among the mutants with severe growth impairment were increased trichome numbers, accumulation of a variety of triterpene saponins, and extensive but differential ectopic expression of defense response genes. No currently proposed model explains the observed phenotypes across all lines. We propose that re-allocation of resources into defense pathways is linked to the severity of the final growth phenotype in monolignol pathway mutants of Medicago, although it remains unclear as to whether this is a cause or an effect of the growth impairment. PMID: 31289215 [PubMed - as supplied by publisher]

Novel pyrrolo[3,2-d]pyrimidine compounds target mitochondrial and cytosolic one-carbon metabolism with broad-spectrum antitumor efficacy.

Thu, 11/07/2019 - 22:40
Novel pyrrolo[3,2-d]pyrimidine compounds target mitochondrial and cytosolic one-carbon metabolism with broad-spectrum antitumor efficacy. Mol Cancer Ther. 2019 Jul 09;: Authors: Dekhne AS, Shah K, Ducker GS, Katinas JM, Wong-Roushar J, Nayeen MJ, Doshi A, Ning C, Bao X, Frühauf J, Liu J, Wallace-Povirk A, O'Connor C, Dzinic SH, White K, Kushner J, Kim S, Hüttemann M, Polin L, Rabinowitz JD, Li J, Hou Z, Dann CE, Gangjee A, Matherly LH Abstract Folate-dependent one-carbon (C1) metabolism is compartmentalized into the mitochondria and cytosol and supports cell growth through nucleotide and amino acid biosynthesis. Mitochondrial C1 metabolism, including serine hydroxymethyltransferase (SHMT) 2, provides glycine, NAD(P)H, ATP, and C1 units for cytosolic biosynthetic reactions, and is implicated in the oncogenic phenotype across a wide range of cancers. Whereas multi-targeted inhibitors of cytosolic C1 metabolism such as pemetrexed are used clinically, there are currently no anticancer drugs that specifically target mitochondrial C1 metabolism. We used molecular modeling to design novel small-molecule pyrrolo[3,2-d]pyrimidine inhibitors targeting mitochondrial C1 metabolism at SHMT2. In vitro antitumor efficacy was established with the lead compounds (AGF291, AGF320, AGF347) toward lung, colon, and pancreatic cancer cells. Intracellular targets were identified by metabolic rescue with glycine and nucleosides, and by targeted metabolomics using a stable isotope tracer, with confirmation by in vitro assays with purified enzymes. In addition to targeting SHMT2, inhibition of the cytosolic purine biosynthetic enzymes, β-glycinamide ribonucleotide formyltransferase and/or 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase, and SHMT1 was also established. AGF347 generated significant in vivo antitumor efficacy with potential for complete responses against both early stage and upstage MIA PaCa-2 pancreatic tumor xenografts, providing compelling proof-of-concept for therapeutic targeting of SHMT2 and cytosolic C1 enzymes by this series. Our results establish structure-activity relationships and identify exciting new drug prototypes for further development as multi-targeted antitumor agents. PMID: 31289137 [PubMed - as supplied by publisher]

Comparison and Discrimination of Artemisia argyi and Artemisia lavandulifolia by Gas Chromatography-Mass Spectrometry-Based Metabolomic Approach.

Thu, 11/07/2019 - 22:40
Comparison and Discrimination of Artemisia argyi and Artemisia lavandulifolia by Gas Chromatography-Mass Spectrometry-Based Metabolomic Approach. J AOAC Int. 2019 Jul 09;: Authors: Guo L, Zhang D, Wang L, Xue Z, Guo M, Duan L, Zheng Y Abstract Background: Artemisia argyi and A. lavandulifolia are two morphologically similar herbal medicines derived from the Artemisia genus. Although the two Artemisia herbs have been used as herbal medicines for a long time, studies on their phytochemicals and bioactive compositions are still limited, and no research has been devoted to compare the volatile compounds in A. argyi and A. lavandulifolia. Objective: To compare the volatile constituents in A. argyi and A. lavandulifolia and to explore chemical markers for discrimination and quality evaluation of the two Artemisia herbal medicines. Methods: A GC-MS-based metabolomic approach was employed to compare and discriminate A. argyi and A. lavandulifolia from the aspect of volatile compounds. Multivariate statistical methods, including principal component analysis and orthogonal partial least-squares discriminate analysis, were applied to explore chemical markers for discrimination of the two Artemisia herbal medicines. Results: Thirty volatile compounds were identified, and the chemical profiles of volatile compounds in A. argyi and A. lavandulifolia were quite similar. Principal component analysis and orthogonal partial least-squares discrimination analysis results indicated that the two Artemisia herbal medicines could be distinguished effectively from each other. Ten volatile compounds were selected as potential chemical markers for discrimination of the two Artemisia herbal medicines. Conclusions: The GC-MS-based metabolomics could be an acceptable strategy for comparison and discrimination of A. argyi and A. lavandulifolia as well as authentication of herbal medicines derived from other closely related species. Highlights: GC-MS based metabolomic approach was firstly applied to compare and discriminate Artemisia argyi and Artemisia lavandulifolia. PMID: 31288892 [PubMed - as supplied by publisher]

Pages