PubMed

Related Articles Mitochondrial Dynamics Controls T Cell Fate through Metabolic Programming. Cell. 2016 Jun 8; Authors: Buck MD, O'Sullivan D, Klein Geltink RI, Curtis JD, Chang CH, Sanin DE, Qiu J, Kretz O, Braas D, van der Windt GJ, Chen Q, Huang SC, O'Neill CM, Edelson BT, Pearce EJ, Sesaki H, Huber TB, Rambold AS, Pearce EL Abstract Activated effector T (TE) cells augment anabolic pathways of metabolism, such as aerobic glycolysis, while memory T (TM) cells engage catabolic pathways, like fatty acid oxidation (FAO). However, signals that drive these differences remain unclear. Mitochondria are metabolic organelles that actively transform their ultrastructure. Therefore, we questioned whether mitochondrial dynamics controls T cell metabolism. We show that TE cells have punctate mitochondria, while TM cells maintain fused networks. The fusion protein Opa1 is required for TM, but not TE cells after infection, and enforcing fusion in TE cells imposes TM cell characteristics and enhances antitumor function. Our data suggest that, by altering cristae morphology, fusion in TM cells configures electron transport chain (ETC) complex associations favoring oxidative phosphorylation (OXPHOS) and FAO, while fission in TE cells leads to cristae expansion, reducing ETC efficiency and promoting aerobic glycolysis. Thus, mitochondrial remodeling is a signaling mechanism that instructs T cell metabolic programming. PMID: 27293185 [PubMed - as supplied by publisher]

Related Articles Evaluation of the Anti-inflammatory Effects of Volatile Oils from Processed Products of Angelica sinensis radix by GC-MS-Based Metabolomics. J Ethnopharmacol. 2016 Jun 9; Authors: Zhong LJ, Hua YL, Ji P, Yao WL, Zhang WQ, Li J, Wei YM Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Roots of Angelica sinensis (Oliv.) Diels (AS) a commonly used herbal，always act as an anti-inflammatory drug in Chinese traditional therapy. In clinical use, AS is always processed before being used for the reason that processing can increase its therapeutic effect. Recent studies have shown that volatile oil of AS (VOAS), an important component in AS, has evident anti-inflammatory activities. AIM OF THE STUDY: In this study, our aim is to evaluate the anti-inflammatory effects of volatile oils from processed products of AS. MATERIALS AND METHODS: In this paper, volatile oils from stir-fried AS (C -VOAS), parched AS with alcohol (J-VOAS), parched AS with soil (T-VOAS), and parched AS with sesame oil (Y-VOAS) were applied to intervene the carrageenan-induced acute inflammation model rats. GC-MS based metabolomics was utilized to determine different metabolites in the inflammatory exudate and plasma samples. RESULTS: The results showed that VOASs could significantly inhibit the release of PGE2, HIS, 5-HT and TNF-α, among which C-VOAS and J-VOAS expressed better effect. Otherwise, 14 potential biomarkers were identified respectively in inflammatory exudate and plasma, which changed highly significantly (P<0.01) in C-VOAS and J-VOAS groups. CONCLUSIONS: We inferred that the anti-inflammatory effect of C-VOAS and J-VOAS were superior to other VOASs. PMID: 27292195 [PubMed - as supplied by publisher]

Related Articles ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9 Authors: Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C Abstract ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46,000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a 'live' website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. PMID: 26467479 [PubMed - indexed for MEDLINE]

Hepatic encephalopathy in ICU: cerebrospinal fluid metabolomics highlights alteration of multiple metabolic pathways representing new potential therapeutic targets. Intensive Care Med Exp. 2015 Dec;3(Suppl 1):A690 Authors: Weiss N, Colsch B, Isnard F, Attala S, Amador M, Lamari F, Sedel F, Junot C, Thabut D, Brain Liver Pitie-Salpetriere Study Group (BLIPS) PMID: 27290266 [PubMed - as supplied by publisher]

Gas chromatography-mass spectrometry metabolomics of goat milk with different polymorphism at the αS1-casein genotype locus. J Dairy Sci. 2016 Jun 8; Authors: Caboni P, Murgia A, Porcu A, Demuru M, Pulina G, Nudda A Abstract Hyphenated gas chromatography-mass spectrometry (GC-MS) and multivariate data analysis techniques were used to uncover milk metabolite differences in different αS1-casein genotypes of goats. By a discriminant GC-MS metabolomics approach, we characterized milk polar metabolites of 28 goats. Animals were selected on the basis of their genotypes as 7 goats classified heterozygous for weak or null alleles, 5 for the genotype EE, 9 for the genotypes AE and BE, and finally 7 for the strong genotype AA. Low molecular weight polar metabolite profile was tightly related to the different goat genotypes, milk production, and protein levels. Results of multivariate statistical analysis of GC-MS data demonstrate that different heterozygous and homozygous genotypes expressed different metabolites such as citric and aconitic acid for the strong allele class with different sugars and polyols for the weak class. PMID: 27289154 [PubMed - as supplied by publisher]

Primary HCMV Infection in Pregnancy from Classic Data towards Metabolomics: an Exploratory analysis. Clin Chim Acta. 2016 Jun 8; Authors: Fattuoni C, Palmas F, Noto A, Barberini L, Mussap M, Grapov D, Dessì A, Casu M, Casanova A, Furione M, Arossa A, Spinillo A, Baldanti F, Fanos V, Zavattoni M Abstract BACKGROUND: Human cytomegalovirus (HCMV) is one of the most frequent risk of viral infections during pregnancy. The aim of this study was to evaluate the metabolic profile in amniotic fluid (AF) samples obtained from HCMV-infected, and uninfected fetuses in order to elucidate changes in metabolic pathways during congenital HCMV infection and to recognize new potential diagnostic and/or prognostic biomarkers. METHODS: A retrospective cohort study was conducted on 63 pregnant women: 20 contracted primary HCMV infection during pregnancy and, subsequently, transmitted the virus to the fetus (transmitters); 20 contracted the infection without transmitting the virus to the fetus (non-transmitters); 23 who underwent amniocentesis for cytogenetic-based diagnosis were considered controls. Metabolomics analysis was performed by using the hyphenated technique Gas chromatography-mass spectrometry (GC-MS) followed by a multivariate statistical approach. Four PLS-DA models were generated: controls vs. transmitters; controls vs. non-transmitters; transmitters vs. non-transmitters; and asymptomatic infected vs. symptomatic infected newborns. Subsequently, these models were exploited for network mapping. RESULTS: Compared with controls, HCMV transmitters showed significantly increased levels in glutamine, glycine, serine, pyruvic acid, threonine, threonic acid, and cystine; conversely, unknown U1715 and U1804, glutamic acid, U1437, fructose, sugar-like A203003 and A203005, and tyrosine levels were found decreased. In non-transmitters, glutamine, serine, glycine, threonic acid, threonine, 1-monostearin, urea, and cystine were found increased, while sorbitol, unknown U1804, sugar-like A203003, U1751, xylitol, leucine and fructose were decreased. The comparison between transmitters and non-transmitters did not produce a statistically significant model. Unlike controls' profile, a common feature of HCMV infected subjects (transmitters and non-transmitters) was the activation of glutamine-glutamate and pyrimidine metabolic pathways. In addition, a clusterization for asymptomatic vs. symptomatic outcome was also observed due to alteration of fatty acids biosynthesis. CONCLUSIONS: Metabolomics approach could highlight the significant modification of maternal and placental status during HCMV infection for both transmitter and non-transmitter subjects. A further separation was observed for asymptomatic vs. symptomatic HCMV congenital infections model. Therefore, metabolomics may be a promising tool to improve the accuracy of an early diagnosis, and the management of HCMV pregnancy-related infections. PMID: 27288986 [PubMed - as supplied by publisher]

Metabolic signatures of Huntington's disease (HD): (1)H NMR analysis of the polar metabolome in post mortem human brain. Biochim Biophys Acta. 2016 Jun 8; Authors: Graham SF, Kumar PK, Bjorndahl T, Han B, Yilmaz A, Sherman E, Bahado-Singh RO, Wishart D, Mann D, Green BD Abstract Huntington's disease (HD) is an autosomal neurodegenerative disorder affecting approximately 5-10 persons per 100,000 worldwide. The pathophysiology of HD is not fully understood but the age of onset is known to be highly dependent on the number of CAG triplet repeats in the huntingtin gene. Using (1)H NMR spectroscopy this study biochemically profiled 39 brain metabolites in post-mortem striatum (n=14) and frontal lobe (n=14) from HD sufferers and controls (n=28). Striatum metabolites were more perturbed with 15 significantly affected in HD cases, compared with only 4 in frontal lobe (P<0.05; q<0.3). The metabolite which changed most overall was urea which decreased 3.25-fold in striatum (P<0.01). Four metabolites were consistently affected in both brain regions. These included the neurotransmitter precursors tyrosine and L-phenylalanine which were significantly depleted by 1.55-1.58-fold and 1.48-1.54-fold in striatum and frontal lobe, respectively (P=0.02-0.03). They also included L-leucine which was reduced 1.54-1.69-fold (P=0.04-0.09) and myo-inositol which was increased 1.26-1.37-fold (P<0.01). Logistic regression analyses performed with MetaboAnalyst demonstrated that data obtained from striatum produced models which were profoundly more sensitive and specific than those produced from frontal lobe. The brain metabolite changes uncovered in this first (1)H NMR investigation of human HD offer new insights into the disease pathophysiology. Further investigations of striatal metabolite disturbances are clearly warranted. PMID: 27288730 [PubMed - as supplied by publisher]

Amino Acids in a Targeted Versus a Non-Targeted Metabolomics LC-MS/MS Assay. Are the Results Consistent? Clin Biochem. 2016 Jun 8; Authors: Klepacki J, Klawitter J, Klawitter J, Karimpour-Fard A, Thurman J, Ingle G, Patel D, Christians U Abstract BACKGROUND: The results of plasma amino acid patterns in samples from kidney transplant patients with good and impaired renal function using a targeted LC-MS/MS amino acid assay and a non-targeted metabolomics assay were compared. METHODS: EDTA plasma samples were prospectively collected at baseline, 1, 2, 4 and 6months post-transplant (n=116 patients, n=398 samples). Each sample was analyzed using both a commercial amino acid LC-MS/MS assay and a non-targeted metabolomics assay also based on MS/MS ion transitions. The results of both assays were independently statistically analyzed to identify amino acids associated with estimated glomerular filtration rates using correlation and partial least squares- discriminant analysis. RESULTS: Although there was overlap between the results of the targeted and non-targeted metabolomics assays (tryptophan, 1-methyl histidine), there were also substantial inconsistencies, with the non-targeted assay resulting in more "hits" than the targeted assay. Without further verification of the hits detected by the non-targeted discovery assay, this would have led to different interpretation of the results. There were also false negative results when the non-targeted assay was used (hydroxy proline). Several of said discrepancies could be explained by loss of sensitivity during analytical runs for selected amino acids (serine and threonine), retention time shifts, signals above the range of linear detector response and integration of peaks not separated from background and interferences (aspartate) when the non-targeted metabolomics assay was used. CONCLUSIONS: Whenever assessment of a specific pathway such as amino acids is the focus of interest, a targeted seems preferable to a non-targeted metabolomics assay. PMID: 27288551 [PubMed - as supplied by publisher]

Metabolite profile of a mouse model of Charcot-Marie-Tooth type 2D neuropathy: implications for disease mechanisms and interventions. Biol Open. 2016 Jun 10; Authors: Bais P, Beebe K, Morelli KH, Currie ME, Norberg SN, Evsikov AV, Miers KE, Seburn KL, Guergueltcheva V, Kremensky I, Jordanova A, Bult CJ, Burgess RW Abstract Charcot-Marie-Tooth disease encompasses a genetically heterogeneous class of heritable polyneuropathies that result in axonal degeneration in the peripheral nervous system. Charcot-Marie-Tooth type 2D neuropathy (CMT2D) is caused by dominant mutations in glycyl tRNA synthetase (GARS). Mutations in the mouse Gars gene result in a genetically and phenotypically valid animal model of CMT2D. How mutations in GARS lead to peripheral neuropathy remains controversial. To identify putative disease mechanisms, we compared metabolites isolated from the spinal cord of Gars mutant mice and their littermate controls. A profile of altered metabolites that distinguish the affected and unaffected tissue was determined. Ascorbic acid was decreased fourfold in the spinal cord of CMT2D mice, but was not altered in serum. Carnitine and its derivatives were also significantly reduced in spinal cord tissue of mutant mice, whereas glycine was elevated. Dietary supplementation with acetyl-L-carnitine improved gross motor performance of CMT2D mice, but neither acetyl-L-carnitine nor glycine supplementation altered the parameters directly assessing neuropathy. Other metabolite changes suggestive of liver and kidney dysfunction in the CMT2D mice were validated using clinical blood chemistry. These effects were not secondary to the neuromuscular phenotype, as determined by comparison with another, genetically unrelated mouse strain with similar neuromuscular dysfunction. However, these changes do not seem to be causative or consistent metabolites of CMT2D, because they were not observed in a second mouse Gars allele or in serum samples from CMT2D patients. Therefore, the metabolite 'fingerprint' we have identified for CMT2D improves our understanding of cellular biochemical changes associated with GARS mutations, but identification of efficacious treatment strategies and elucidation of the disease mechanism will require additional studies. PMID: 27288508 [PubMed - as supplied by publisher]

Systematic Molecular Phenotyping: A Path Towards Precision Emergency Medicine? Acad Emerg Med. 2016 Jun 11; Authors: Limkakeng AT, Monte A, Kabrhel C, Puskarich M, Heitsch L, Tsalik EL, Shapiro NI Abstract Precision medicine is an emerging approach to disease treatment and prevention that considers variability in patient genes, environment, and lifestyle. However, little has been written about how such research impacts emergency care. Recent advances in analytical techniques have made it possible to characterize patients in a more comprehensive and sophisticated fashion at the molecular level, promising highly individualized diagnosis and treatment. Among these techniques are various systematic molecular phenotyping analyses (e.g., genomics, transcriptomics, proteomics, and metabolomics). Although a number of emergency physicians use such techniques in their research, widespread discussion of these approaches has been lacking in the emergency care literature and many emergency physicians may be unfamiliar with them. In this article, we briefly review the underpinnings of such studies, note how they already impact acute care, discuss areas in which they might soon be applied, and identify challenges in translation to the emergency department. While such techniques hold much promise, it is unclear whether the obstacles to translating their findings to the emergency department will be overcome in the near future. Such obstacles include validation, cost, turnaround time, user interface, decision support, standardization, and adoption by end users. This article is protected by copyright. All rights reserved. PMID: 27288269 [PubMed - as supplied by publisher]

ALG6-CDG: a recognizable phenotype with epilepsy, proximal muscle weakness, ataxia and behavioral and limb anomalies. J Inherit Metab Dis. 2016 Jun 10; Authors: Morava E, Tiemes V, Tiel C, Seta N, de Lonlay P, de Klerk H, Mulder M, Rubio-Gozalbo E, Visser G, van Hasselt P, Horovitz DD, de Souza CF, Schwartz IV, Green A, Al-Owain M, Uziel G, Sigaudy S, Chabrol B, van Spronsen FJ, Steinert M, Komini E, Wurm D, Bevot A, Ayadi A, Huijben K, Dercksen M, Witters P, Jaeken J, Matthijs G, Lefeber DJ, Wevers RA Abstract INTRODUCTION: Alpha-1,3-glucosyltransferase congenital disorder of glycosylation (ALG6-CDG) is a congenital disorder of glycosylation. The original patients were described with hypotonia, developmental disability, epilepsy, and increased bleeding tendency. METHODS: Based on Euroglycan database registration, we approached referring clinicians and collected comprehensive data on 41 patients. RESULTS: We found hypotonia and developmental delay in all ALG6-CDG patients and epilepsy, ataxia, proximal muscle weakness, and, in the majority of cases, failure to thrive. Nine patients developed intractable seizures. Coagulation anomalies were present in <50 % of cases, without spontaneous bleedings. Facial dysmorphism was rare, but seven patients showed missing phalanges and brachydactyly. Cyclic behavioral change, with autistic features and depressive episodes, was one of the most significant complaints. Eleven children died before the age of 4 years due to protein losing enteropathy (PLE), sepsis, or seizures. The oldest patient was a 40 year-old Dutch woman. The most common pathogenic protein alterations were p.A333V and p.I299Del, without any clear genotype-phenotype correlation. DISCUSSION: ALG6-CDG has been now described in 89 patients, making it the second most common type of CDG. It has a recognizable phenotype and a primary neurologic presentation. PMID: 27287710 [PubMed - as supplied by publisher]

Metabolic characterization of the natural progression of chronic hepatitis B. Genome Med. 2016;8(1):64 Authors: Schoeman JC, Hou J, Harms AC, Vreeken RJ, Berger R, Hankemeier T, Boonstra A Abstract BACKGROUND: Worldwide, over 350 million people are chronically infected with the hepatitis B virus (HBV) and are at increased risk of developing progressive liver diseases. The confinement of HBV replication to the liver, which also acts as the central hub for metabolic and nutritional regulation, emphasizes the interlinked nature of host metabolism and the disease. Still, the metabolic processes operational during the distinct clinical phases of a chronic HBV infection-immune tolerant, immune active, inactive carrier, and HBeAg-negative hepatitis phases-remains unexplored. METHODS: To investigate this, we conducted a targeted metabolomics approach on serum to determine the metabolic progression over the clinical phases of chronic HBV infection, using patient samples grouped based on their HBV DNA, alanine aminotransferase, and HBeAg serum levels. RESULTS: Our data illustrate the strength of metabolomics to provide insight into the metabolic dysregulation experienced during chronic HBV. The immune tolerant phase is characterized by the speculated viral hijacking of the glycerol-3-phosphate-NADH shuttle, explaining the reduced glycerophospholipid and increased plasmalogen species, indicating a strong link to HBV replication. The persisting impairment of the choline glycerophospholipids, even during the inactive carrier phase with minimal HBV activity, alludes to possible metabolic imprinting effects. The progression of chronic HBV is associated with increased concentrations of very long chain triglycerides together with citrulline and ornithine, reflective of a dysregulated urea cycle peaking in the HBV envelope antigen-negative phase. CONCLUSIONS: The work presented here will aid in future studies to (i) validate and understand the implication of these metabolic changes using a thorough systems biology approach, (ii) monitor and predict disease severity, as well as (iii) determine the therapeutic value of the glycerol-3-phosphate-NADH shuttle. PMID: 27286979 [PubMed - as supplied by publisher]

Metabolomics study of renal fibrosis and intervention effects of total aglycone extracts of Scutellaria baicalensis in unilateral ureteral obstruction rats. J Ethnopharmacol. 2016 Jun 7; Authors: Fang J, Wang W, Sun S, Wang Y, Li Q, Lu X, Qiu M, Zhang Y Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Scutellariae Radix (Scutellaria baicalensis Georgi) is a well-known traditional Chinese medicine (TCM) which mainly contains flavonoids. Our previous studies have demonstrated that total aglycone extracts of Scutellaria Baicalensis (TAES) can improve kidney disease in rats. AIM OF THE STUDY: To investigate the renal fibrosis (RF) pathogenesis and TAES treatment mechanism in unilateral ureteral obstruction (UUO) rats, using a metabolomics approach based on gas chromatography-mass spectrometry (GC/MS). METHODS: Rats with RF were divided into 6 groups with rats subjected to sham operation as normal control. The effects of TAES on some RF closely related parameters in UUO rats were investigated. A metabolomics method, based on GC/MS, was developed to monitor metabolic alterations in urine. Multivariate data analysis was utilized to identify biomarkers potentially associated with RF and the anti-RF activity of TAES. Ontology-based enrichment analysis by BiNChE and pathway analysis by MetPA aid in the interpretation of difference metabolites. RESULTS: After ten days of treatment, the parameters of renal function begin returning to normal, and the abnormal high expressions of genes associated with extracellular matrix (ECM) were relived. In the metabolomics study, metabolic perturbations induced by UUO were reversed after treatment and TAES showed a dose-dependent therapy effect on RF, meanwhile, 18 potential biomarkers associated with RF were identified. Enrichment analysis of metabolites shows an over representation of mostly alkane-alpha, omega-diamine and alpha, omega-dicarboxylic acid, and these biomarkers are primarily involved in Glycine, serine and threonine metabolism, Retinol metabolism, Arginine and proline metabolism and Fructose and mannose metabolism. CONCLUSIONS: Our findings indicate that TAES have positive effects on UUO-induced RF in rats, meanwhile, metabolomics method coupled with metabolites enrichment analysis is a useful tool for revealing the pathogenesis of diseases and action mechanism of TCM on the whole body. PMID: 27286917 [PubMed - as supplied by publisher]

Potential Health Benefits and Metabolomics of Camel Milk by GC-MS and ICP-MS. Biol Trace Elem Res. 2016 Jun 11; Authors: Ahamad SR, Raish M, Ahmad A, Shakeel F Abstract None of the research reports reveals the metabolomics and elemental studies on camel milk. Recent studies showed that camel milk possesses anticancer and anti-inflammatory activity. Metabolomics and elemental studies were carried out in camel milk which showed us the pathways and composition that are responsible for the key biological role of camel milk. Camel milk was dissolved in methanol and chloroform fraction and then vortexed and centrifuged. Both the fractions were derivatized by N,O-bis-(trimethylsilyl)trifluoroacetamide (BSTFA) and TMCS after nitrogen purging and analyzed by GC-MS. Camel milk was also analyzed by ICP-MS after microwave digestion. We found that higher alkanes and fatty acids are present in the chloroform fraction and amino acids, sugars and fatty acid derivatives are present in aqueous fractions. All the heavy metals like As, Pb, Cd, Co, Cu, and Ni were in the safe limits in terms of maximum daily intake of these elements. Na, K, Mg, and Ca were also present in the safe limits in terms of maximum daily intake of these elements. These results suggested that the camel milk drinking is safe and there is no health hazard. The present data of GC-MS and ICP-MS correlate the activities related to camel milk. PMID: 27286716 [PubMed - as supplied by publisher]

HORSE SPECIES SYMPOSIUM: Canine intestinal microbiology and metagenomics: From phylogeny to function. J Anim Sci. 2016 Jun;94(6):2247-2261 Authors: Guard BC, Suchodolski JS Abstract Recent molecular studies have revealed a complex microbiota in the dog intestine. Convincing evidence has been reported linking changes in microbial communities to acute and chronic gastrointestinal inflammation, especially in canine inflammatory bowel disease (IBD). The most common microbial changes observed in intestinal inflammation are decreases in the bacterial phyla Firmicutes (i.e., Lachnospiraceae, Ruminococcaceae, and ) and Bacteroidetes, with concurrent increases in Proteobacteria (i.e., ). Due to the important role of microbial-derived metabolites for host health, it is important to elucidate the metabolic consequences of gastrointestinal dysbiosis and physiological pathways implicated in specific disease phenotypes. Metagenomic studies have used shotgun sequencing of DNA as well as phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to characterize functional changes in the bacterial metagenome in gastrointestinal disease. Furthermore, wide-scale and untargeted measurements of metabolic products derived by the host and the microbiota in intestinal samples allow a better understanding of the functional alterations that occur in gastrointestinal disease. For example, changes in bile acid metabolism and tryptophan catabolism recently have been reported in humans and dogs. Also, metabolites associated with the pentose phosphate pathway were significantly altered in chronic gastrointestinal inflammation and indicate the presence of oxidative stress in dogs with IBD. This review focuses on the advancements made in canine metagenomics and metabolomics and their implications in understanding gastrointestinal disease as well as the development of better treatment approaches. PMID: 27285902 [PubMed - as supplied by publisher]

Systems proteomics of liver mitochondria function. Science. 2016 Jun 10;352(6291):aad0189 Authors: Williams EG, Wu Y, Jha P, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J Abstract Recent improvements in quantitative proteomics approaches, including Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), permit reproducible large-scale protein measurements across diverse cohorts. Together with genomics, transcriptomics, and other technologies, transomic data sets can be generated that permit detailed analyses across broad molecular interaction networks. Here, we examine mitochondrial links to liver metabolism through the genome, transcriptome, proteome, and metabolome of 386 individuals in the BXD mouse reference population. Several links were validated between genetic variants toward transcripts, proteins, metabolites, and phenotypes. Among these, sequence variants in Cox7a2l alter its protein's activity, which in turn leads to downstream differences in mitochondrial supercomplex formation. This data set demonstrates that the proteome can now be quantified comprehensively, serving as a key complement to transcriptomics, genomics, and metabolomics--a combination moving us forward in complex trait analysis. PMID: 27284200 [PubMed - in process]

'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites. Biochem Soc Trans. 2016 Jun 15;44(3):961-71 Authors: Lerma-Ortiz C, Jeffryes JG, Cooper AJ, Niehaus TD, Thamm AM, Frelin O, Aunins T, Fiehn O, de Crécy-Lagard V, Henry CS, Hanson AD Abstract Many common metabolites are intrinsically unstable and reactive, and hence prone to chemical (i.e. non-enzymatic) damage in vivo Although this fact is widely recognized, the purely chemical side-reactions of metabolic intermediates can be surprisingly hard to track down in the literature and are often treated in an unprioritized case-by-case way. Moreover, spontaneous chemical side-reactions tend to be overshadowed today by side-reactions mediated by promiscuous ('sloppy') enzymes even though chemical damage to metabolites may be even more prevalent than damage from enzyme sloppiness, has similar outcomes, and is held in check by similar biochemical repair or pre-emption mechanisms. To address these limitations and imbalances, here we draw together and systematically integrate information from the (bio)chemical literature, from cheminformatics, and from genome-scale metabolic models to objectively define a 'Top 30' list of damage-prone metabolites. A foundational part of this process was to derive general reaction rules for the damage chemistries involved. The criteria for a 'Top 30' metabolite included predicted chemical reactivity, essentiality, and occurrence in diverse organisms. We also explain how the damage chemistry reaction rules ('operators') are implemented in the Chemical-Damage-MINE (CD-MINE) database (minedatabase.mcs.anl.gov/#/top30) to provide a predictive tool for many additional potential metabolite damage products. Lastly, we illustrate how defining a 'Top 30' list can drive genomics-enabled discovery of the enzymes of previously unrecognized damage-control systems, and how applying chemical damage reaction rules can help identify previously unknown peaks in metabolomics profiles. PMID: 27284066 [PubMed - in process]

Metabolic and antioxidant profiles of herbal infusions and decoctions. Food Chem. 2016 Nov 15;211:963-71 Authors: Fotakis C, Tsigrimani D, Tsiaka T, Lantzouraki DZ, Strati IF, Makris C, Tagkouli D, Proestos C, Sinanoglou VJ, Zoumpoulakis P Abstract This study implements NMR metabolomics and spectrophotometric studies (Folin-Ciocalteu, FRAP, ABTS) to infusions and decoctions of ten plant species in order to assess and compare the metabolic and antioxidant profiles for each botanical family. Multivariate and univariate data analyses highlighted the differences among the samples and pinpointed specific classes of compounds for each plant species as well as infusions and decoctions. The identified phenolic compounds by NMR, as well as the antioxidant profile, framed a trend of increased values in infusions compared to the decoctions. Moreover, the infusion procedure positively affected the extractability of the phenolic compounds compared to decoctions. The highest total phenolic content was found in Mentha spicata, while the lowest in Matricaria chamomilla preparations, irrespective of the preparation method. The preparation time for the decoctions was examined showing that the 15min preparations were generally found richer in phenolics and of higher antioxidant capacity. PMID: 27283718 [PubMed - in process]

New integrative computational approaches unveil the Saccharomyces cerevisiae pheno-metabolomic fermentative profile and allow strain selection for winemaking. Food Chem. 2016 Nov 15;211:509-20 Authors: Franco-Duarte R, Umek L, Mendes I, Castro CC, Fonseca N, Martins R, Silva-Ferreira AC, Sampaio P, Pais C, Schuller D Abstract During must fermentation by Saccharomyces cerevisiae strains thousands of volatile aroma compounds are formed. The objective of the present work was to adapt computational approaches to analyze pheno-metabolomic diversity of a S. cerevisiae strain collection with different origins. Phenotypic and genetic characterization together with individual must fermentations were performed, and metabolites relevant to aromatic profiles were determined. Experimental results were projected onto a common coordinates system, revealing 17 statistical-relevant multi-dimensional modules, combining sets of most-correlated features of noteworthy biological importance. The present method allowed, as a breakthrough, to combine genetic, phenotypic and metabolomic data, which has not been possible so far due to difficulties in comparing different types of data. Therefore, the proposed computational approach revealed as successful to shed light into the holistic characterization of S. cerevisiae pheno-metabolome in must fermentative conditions. This will allow the identification of combined relevant features with application in selection of good winemaking strains. PMID: 27283661 [PubMed - in process]

Different metabolic responses to PI3K inhibition in NSCLC cells harboring wild-type and G12C mutant KRAS. Oncotarget. 2016 Jun 6; Authors: Caiola E, Brunelli L, Marabese M, Broggini M, Lupi M, Pastorelli R Abstract KRAS mutations in non-small-cell lung cancer (NSCLC) patients are considered a negative predictive factor and indicate poor response to anticancer treatments. KRAS mutations lead to activation of the PI3K/akt/mTOR pathway, whose inhibition remains a challenging clinical target. Since the PI3K/akt/mTOR pathway and KRAS oncogene mutations all have roles in cancer cell metabolism, we investigated whether the activity of PI3K/akt/mTOR inhibitors (BEZ235 and BKM120) in cells harboring different KRAS status is related to their metabolic effect. Isogenic NSCLC cell clones expressing wild-type (WT) and mutated (G12C) KRAS were used to determine the response to BEZ235 and BKM120. Metabolomics analysis indicated the impairment of glutamine in KRAS-G12C and serine metabolism in KRAS-WT, after pharmacological blockade of the PI3K signaling, although the net effect on cell growth, cell cycle distribution and caspase activation was similar. PI3K inhibitors caused autophagy in KRAS-WT, but not in KRAS-G12C, where there was a striking decrease in ammonia production, probably a consequence of glutamine metabolism impairment.These findings lay the grounds for more effective therapeutic combinations possibly distinguishing wild-type and mutated KRAS cancer cells in NSCLC, exploiting their different metabolic responses to PI3K/akt/mTOR inhibitors. PMID: 27283493 [PubMed - as supplied by publisher]