PubMed

Enabling Metabolomics Based Biomarker Discovery Studies Using Molecular Phenotyping of Exosome-Like Vesicles. PLoS One. 2016;11(3):e0151339 Authors: Altadill T, Campoy I, Lanau L, Gill K, Rigau M, Gil-Moreno A, Reventos J, Byers S, Colas E, Cheema AK Abstract Identification of sensitive and specific biomarkers with clinical and translational utility will require smart experimental strategies that would augment expanding the breadth and depth of molecular measurements within the constraints of currently available technologies. Exosomes represent an information rich matrix to discern novel disease mechanisms that are thought to contribute to pathologies such as dementia and cancer. Although proteomics and transcriptomic studies have been reported using Exosomes-Like Vesicles (ELVs) from different sources, exosomal metabolome characterization and its modulation in health and disease remains to be elucidated. Here we describe methodologies for UPLC-ESI-MS based small molecule profiling of ELVs from human plasma and cell culture media. In this study, we present evidence that indeed ELVs carry a rich metabolome that could not only augment the discovery of low abundance biomarkers but may also help explain the molecular basis of disease progression. This approach could be easily translated to other studies seeking to develop predictive biomarkers that can subsequently be used with simplified targeted approaches. PMID: 26974972 [PubMed - as supplied by publisher]

Dissect style response to pollination using metabolite profiling in self-compatible and self-incompatible tomato species. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Feb 23;1017-1018:153-162 Authors: Zhao P, Pan Q, Yu W, Zhao L Abstract Tomato style is the pathway for pollen germination and pollen tubes growth from the stigma to the ovules where fertilization occurs. It is essential to supplying the nutrients for pollen tube growth and guidance for the pollen tubes. To our knowledge, style also regulates gametophytic self-incompatibility (SI) in tomato species. This study identified the metabolites and monitored the metabolic changes of self-incompatible and self-compatible tomato with self-pollinated or unpollinated styles by gas chromatography-mass spectrometry (GC-MS). A total of 9 classes of compounds were identified in SI and self-compatibility (SC) self-pollinated and unpollinated styles which included amino acids, sugars, fatty acids/lipids, amines, organic acids, alcohols, nitriles, inorganic acids and other compounds. The contents of d-Mannose-6-phosphate, Cellobiose, Myristic acid, 2,4-Diaminobutyric acid, Inositol and Urea were significantly decreased and the rest did not significantly change in SI styles. But change of metabolites content significantly happened in SC styles. In addition, among the total 9 classes of compounds, the different metabolites accounted for a different proportion in amino acids, sugars, amines, organic acids and alcohols compared SC and SI. The result indicated that the physiological changes of styles existed differences in SC and SI after self pollination. PMID: 26974868 [PubMed - as supplied by publisher]

Impaired 17,20-lyase activity in male mice lacking cytochrome b5 in Leydig cells. Mol Endocrinol. 2016 Mar 14;:me20151282 Authors: Sondhi V, Owen BM, Liu J, Chomic R, Kliewer SA, Hughes BA, Arlt W, Mangelsdorf DJ, Auchus RJ Abstract Androgen and estrogen biosynthesis in mammals requires the 17,20-lyase activity of cytochrome P450 17A1 (steroid 17-hydroxylase/17,20-lyase, CYP17A1). Maximal 17,20-lyase activity in vitro requires the presence of cytochrome b5 (b5), and rare cases of b5 deficiency in human beings causes isolated 17,20-lyase deficiency. To study the consequences of conditional b5 removal from testicular Leydig cells in an animal model, we generated Cyb5(flox/flox):Sf1-Cre (LeyKO) mice. The LeyKO male mice had normal body weights, testis and sex organ weights, and fertility compared to littermates. Basal serum and urine steroid profiles of LeyKO males were not significantly different than littermates. In contrast, marked 17-hydroxyprogesterone (17OHP) accumulation (100-fold basal) and reduced testosterone synthesis (27% of littermates) were observed following hCG stimulation in LeyKO animals. Testis homogenates from LeyKO mice showed reduced 17,20-lyase activity and a 3-fold increased 17-hydroxylase/17,20-lyase activity ratio, which were restored to normal upon addition of recombinant b5. We conclude that Leydig cell b5 is required for maximal androgen synthesis and to prevent 17OHP accumulation in the mouse testis; however, the b5-independent 17,20-lyase activity of mouse P450 17A1 is sufficient for normal male genital development and fertility. LeyKO male mice are a good model for the biochemistry but not the physiology of isolated 17,20-lyase deficiency in human beings. PMID: 26974035 [PubMed - as supplied by publisher]

GATA4 regulates blood-testis barrier function and lactate metabolism in mouse Sertoli cells. Endocrinology. 2016 Mar 14;:en20151927 Authors: Schrade A, Kyrönlahti A, Akinrinade O, Pihlajoki M, Fischer S, Rodriguez VM, Otte K, Velagapudi V, Toppari J, Wilson DB, Heikinheimo M Abstract Conditional deletion of Gata4 in Sertoli cells (SCs) of adult mice has been shown to increase permeability of the blood-testis barrier (BTB) and disrupt spermatogenesis. To gain insight into the molecular underpinnings of these phenotypic abnormalities, we assessed the impact of Gata4 gene silencing in cell culture models. Microarray hybridization identified genes dysregulated by siRNA-mediated inhibition of Gata4 in TM4 cells, an immortalized mouse SC line. Differentially expressed genes were validated by qRT-PCR analysis of primary cultures of Gata4(flox/flox) mouse SCs that had been subjected to cre-mediated recombination in vitro. Depletion of GATA4 in TM4 cells and primary SCs was associated with altered expression of genes involved in key facets of BTB maintenance, including tight/adherens junction formation (Tjp1, Cldn12, Vcl, Tnc, Csk) and extracellular matrix reorganization (Lamc1, Col4a1, Col4a5, Mmp10, Mmp23, Timp2). Western blotting and immunocytochemistry demonstrated reduced levels of TJP1, a prototypical tight junction protein, in GATA4-depleted cells. These changes were accompanied by a loss of morphologically-recognizable junctional complexes and a decline in trans-epithelial membrane resistance. Furthermore, Gata4 gene silencing was associated with altered expression of Hk1, Gpi1, Pfkp, Pgam1, Gls2, Pdk3, Pkd4, and Ldhb, genes regulating the production of lactate, a key nutrient that SCs provide to developing germ cells. Comprehensive metabolomic profiling demonstrated impaired lactate production in GATA4-deficient SCs. We conclude that GATA4 plays a pivotal role in the regulation of BTB function and lactate metabolism in mouse SCs. PMID: 26974005 [PubMed - as supplied by publisher]

The potential relevance of the endocannabinoid, 2-arachidonoylglycerol, in diffuse large B-cell lymphoma. Oncoscience. 2016;3(1):31-41 Authors: Zhang J, Medina-Cleghorn D, Bernal-Mizrachi L, Bracci PM, Hubbard A, Conde L, Riby J, Nomura DK, Skibola CF Abstract Diffuse large B-cell lymphoma is an aggressive, genetically heterogenerous disease and the most common type of non-Hodgkin lymphoma among adults. To gain further insights into the etiology of DLBCL and to discover potential disease-related factors, we performed a serum lipid analysis on a subset of individuals from a population-based NHL case-control study. An untargeted mass-spectrometry-based metabolomics platform was used to analyze serum samples from 100 DLBCL patients and 100 healthy matched controls. Significantly elevated levels of the endocannabinoid, 2-arachidonoylglycerol (2-AG), were detected in the serum of DLBCL patients (121%, P < 0.05). In the male controls, elevated 2-AG levels were observed in those who were overweight (BMI ≥ 25 - < 30 kg/m2; 108%, P < 0.01) and obese (BMI ≥ 30 kg/m(2); 118%, P < 0.001) compared to those with a BMI < 25 kg/m(2). DLBCL cell lines treated with exogenous 2-AG across a range of concentrations, exhibited heterogenous responses: proliferation rates were markedly higher in 4 cell lines by 22%-68% (P < 0.001) and lower in 8 by 20%-75% (P < 0.001). The combined findings of elevated 2-AG levels in DLBCL patients and the proliferative effects of 2-AG on a subset of DLBCL cell lines suggests that 2-AG may play a potential role in the pathogenesis or progression of a subset of DLBCLs. PMID: 26973858 [PubMed]

Metabolomics and Its Application to Acute Lung Diseases. Front Immunol. 2016;7:44 Authors: Stringer KA, McKay RT, Karnovsky A, Quémerais B, Lacy P Abstract Metabolomics is a rapidly expanding field of systems biology that is gaining significant attention in many areas of biomedical research. Also known as metabonomics, it comprises the analysis of all small molecules or metabolites that are present within an organism or a specific compartment of the body. Metabolite detection and quantification provide a valuable addition to genomics and proteomics and give unique insights into metabolic changes that occur in tangent to alterations in gene and protein activity that are associated with disease. As a novel approach to understanding disease, metabolomics provides a "snapshot" in time of all metabolites present in a biological sample such as whole blood, plasma, serum, urine, and many other specimens that may be obtained from either patients or experimental models. In this article, we review the burgeoning field of metabolomics in its application to acute lung diseases, specifically pneumonia and acute respiratory disease syndrome (ARDS). We also discuss the potential applications of metabolomics for monitoring exposure to aerosolized environmental toxins. Recent reports have suggested that metabolomics analysis using nuclear magnetic resonance (NMR) and mass spectrometry (MS) approaches may provide clinicians with the opportunity to identify new biomarkers that may predict progression to more severe disease, such as sepsis, which kills many patients each year. In addition, metabolomics may provide more detailed phenotyping of patient heterogeneity, which is needed to achieve the goal of precision medicine. However, although several experimental and clinical metabolomics studies have been conducted assessing the application of the science to acute lung diseases, only incremental progress has been made. Specifically, little is known about the metabolic phenotypes of these illnesses. These data are needed to substantiate metabolomics biomarker credentials so that clinicians can employ them for clinical decision-making and investigators can use them to design clinical trials. PMID: 26973643 [PubMed]

Murine Depression Model and its Potential Applications for Discovering Foods and Farm Products with Antidepressant-Like Effects. Front Neurosci. 2016;10:72 Authors: Goto T, Tomonaga S, Okayama T, Toyoda A Abstract Advanced societies face increased health problems related to various stresses. Chronic psychological stress is a major risk factor for psychiatric disorders such as depression. Although therapeutic agents reduce several symptoms of depression, most have side effects in a broad range of the population. Furthermore, some victims of depression do not show significant improvement with any drugs, so alternative approaches are needed. Good dietary habits may potentially reduce depressive symptoms, but there is little scientific evidence thus far. Murine depression models are useful to test nutritional approaches in vivo. Our model mice subjected to a subchronic mild social defeat stress (sCSDS) paradigm show several alterations in physiological parameters and social behavior. These stress-induced symptoms in sCSDS mice can be used as cues to identify antidepressant-like natural resources including foods and farm products. We previously discovered that sCSDS mice show more vulnerability to social stress by changing dietary condition. In addition, we developed a more objective system for analyzing mouse behavior using a 3D depth-sensing camera to understand relationships between diet and behavior. The combination of sCSDS mice with 3D behavioral analysis is a powerful method for screening ingredients in foods and farm products for antidepressant-like effects. PMID: 26973450 [PubMed]

The metabolomic detection of lung cancer biomarkers in sputum. Lung Cancer. 2016 Apr;94:88-95 Authors: Cameron SJ, Lewis KE, Beckmann M, Allison GG, Ghosal R, Lewis PD, Mur LA Abstract OBJECTIVES: Developing screening and diagnosis methodologies based on novel biomarkers should allow for the detection of the lung cancer (LC) and possibly at an earlier stage and thereby increase the effectiveness of clinical interventions. Here, our primary objective was to evaluate the potential of spontaneous sputum as a source of non-invasive metabolomic biomarkers for LC status. MATERIALS AND METHODS: Spontaneous sputum was collected and processed from 34 patients with suspected LC, alongside 33 healthy controls. Of the 34 patients, 23 were subsequently diagnosed with LC (LC(+), 16 NSCLC, six SCLC, and one radiological diagnosis), at various stages of disease progression. The 67 samples were analysed using flow infusion electrospray ion mass spectrometry (FIE-MS) and gas-chromatography mass spectrometry (GC-MS). RESULTS: Principal component analysis identified negative mode FIE-MS as having the main separating power between samples from healthy and LC. Discriminatory metabolites were identified using ANOVA and Random Forest. Indications of potential diagnostic accuracy involved the use of receiver operating characteristic/area under the curve (ROC/AUC) analyses. This approach identified metabolites changes that were only observed with LC. Metabolites with AUC values of greater than 0.8 which distinguished between LC(+)/LC(-) binary classifications where identified and included Ganglioside GM1 which has previously been linked to LC. CONCLUSION: This study indicates that metabolomics based on sputum can yield metabolites that can be used as a diagnostic and/or discriminator tool. These could aid clinical intervention and targeted diagnosis of LC within an 'at risk' LC(-) population group. The use of sputum as a non-invasive source of metabolite biomarkers may aid in the development of an at-risk population screening programme for lung cancer or enhanced clinical diagnostic pathways. PMID: 26973212 [PubMed - in process]

The Oxygen Sensor PHD2 Controls Dendritic Spines and Synapses via Modification of Filamin A. Cell Rep. 2016 Mar 8; Authors: Segura I, Lange C, Knevels E, Moskalyuk A, Pulizzi R, Eelen G, Chaze T, Tudor C, Boulegue C, Holt M, Daelemans D, Matondo M, Ghesquière B, Giugliano M, Ruiz de Almodovar C, Dewerchin M, Carmeliet P Abstract Neuronal function is highly sensitive to changes in oxygen levels, but how hypoxia affects dendritic spine formation and synaptogenesis is unknown. Here we report that hypoxia, chemical inhibition of the oxygen-sensing prolyl hydroxylase domain proteins (PHDs), and silencing of Phd2 induce immature filopodium-like dendritic protrusions, promote spine regression, reduce synaptic density, and decrease the frequency of spontaneous action potentials independently of HIF signaling. We identified the actin cross-linker filamin A (FLNA) as a target of PHD2 mediating these effects. In normoxia, PHD2 hydroxylates the proline residues P2309 and P2316 in FLNA, leading to von Hippel-Lindau (VHL)-mediated ubiquitination and proteasomal degradation. In hypoxia, PHD2 inactivation rapidly upregulates FLNA protein levels because of blockage of its proteasomal degradation. FLNA upregulation induces more immature spines, whereas Flna silencing rescues the immature spine phenotype induced by PHD2 inhibition. PMID: 26972007 [PubMed - as supplied by publisher]

Lipoprotein subfractions by nuclear magnetic resonance are associated with tumor characteristics in breast cancer. Lipids Health Dis. 2016;15(1):56 Authors: Flote VG, Vettukattil R, Bathen TF, Egeland T, McTiernan A, Frydenberg H, Husøy A, Finstad SE, Lømo J, Garred Ø, Schlichting E, Wist EA, Thune I Abstract BACKGROUND: High-Density Lipoprotein (HDL)-cholesterol, has been associated with breast cancer development, but the association is under debate, and whether lipoprotein subfractions is associated with breast tumor characteristics remains unclear. METHODS: Among 56 women with newly diagnosed invasive breast cancer stage I/II, aged 35-75 years, pre-surgery overnight fasting serum concentrations of lipids were assessed, and body mass index (BMI) was measured. All breast tumors were immunohistochemically examined in the surgical specimen. Serum metabolomics of lipoprotein subfractions and their contents of cholesterol, free cholesterol, phospholipids, apolipoprotein-A1 and apolipoprotein-A2, were assessed using nuclear magnetic resonance. Principal component analysis, partial least square analysis, and uni- and multivariable linear regression models were used to study whether lipoprotein subfractions were associated with breast cancer tumor characteristics. RESULTS: The breast cancer patients had following means: age at diagnosis: 55.1 years; BMI: 25.1 kg/m(2); total-Cholesterol: 5.74 mmol/L; HDL-Cholesterol: 1.78 mmol/L; Low-Density Lipoprotein (LDL)-Cholesterol: 3.45 mmol/L; triglycerides: 1.18 mmol/L. The mean tumor size was 16.4 mm, and the mean Ki67 hotspot index was 26.5 %. Most (93 %) of the patients had estrogen receptor (ER) positive tumors (≥1 % ER+), and 82 % had progesterone receptor (PgR) positive tumors (≥10 % PgR+). Several HDL subfraction contents were strongly associated with PgR expression: Apolipoprotein-A1 (β 0.46, CI 0.22-0.69, p < 0.001), HDL cholesterol (β 0.95, CI 0.51-1.39, p < 0.001), HDL free cholesterol (β 2.88, CI 1.28-4.48, p = 0.001), HDL phospholipids (β 0.70, CI 0.36-1.04, p < 0.001). Similar results were observed for the subfractions of HDL1-3. We observed inverse associations between HDL phospholipids and Ki67 (β -0.25, p = 0.008), and in particular between HDL1's contents of cholesterol, phospholipids, apolipoprotein-A1, apolipoprotein-A2 and Ki67. No association was observed between lipoproteins and ER expression. CONCLUSION: Our findings hypothesize associations between different lipoprotein subfractions, and PgR expression, and Ki 67 % in breast tumors. These findings may have clinical implications, but require confirmation in larger studies. PMID: 26970778 [PubMed - as supplied by publisher]

Related Articles Gene-gene and gene-environment interactions on risk of male infertility: Focus on the metabolites. Environ Int. 2016 Mar 9;91:188-195 Authors: Hu W, Chen M, Wu W, Lu J, Zhao D, Pan F, Lu C, Xia Y, Hu L, Chen D, Sha J, Wang X Abstract Infertility affects about 17% couples, and males contribute to half of the cases. Compared with independent effects of genetic and environmental factors, interactions between them help in the understanding of the susceptibility to male infertility. Thus, we genotyped 25 polymorphisms, measured 16 urinary chemical concentrations and explored interactions between gene-gene and gene-environment in 1039 Han Chinese using metabolomic analysis. We first observed that GSTT1 might interact with GSTM1 (Pinter=6.33×10(-8)). Furthermore, an interaction between GSTM1 and 4-n-octylphenol (4-n-OP) was identified (Pinter=7.00×10(-3)), as well as a 2-order interaction among GSTT1, GSTM1 and 4-n-OP (Pinter=0.04). Subjects with GSTT1-present and GSTM1-null genotypes were susceptible to male infertility when exposed to 4-n-OP (OR=14.05, 95% CI=4.78-60.20, P=2.34×10(-5)). Most metabolites identified were involved in the tricarboxylic acid cycle. In conclusion, it is a novel study of the interaction on male infertility from the aspect of metabolomics. PMID: 26970590 [PubMed - as supplied by publisher]

Related Articles Product ion isotopologue pattern: A tool to improve the reliability of elemental composition elucidations of unknown compounds in complex matrices. Rapid Commun Mass Spectrom. 2016 Apr 15;30(7):791-799 Authors: Kaufmann A, Walker S, Mol G Abstract RATIONALE: Elucidation of the elemental compositions of unknown compounds (e.g., in metabolomics) generally relies on the availability of accurate masses and isotopic ratios. This study focuses on the information provided by the abundance ratio within a product ion pair (monoisotopic versus the first isotopic peak) when isolating and fragmenting the first isotopic ion (first isotopic mass spectrum) of the precursor. METHODS: This process relies on the capability of the quadrupole within the Q Orbitrap instrument to isolate a very narrow mass window. Selecting only the first isotopic peak (first isotopic mass spectrum) leads to the observation of a unique product ion pair. The lighter ion within such an isotopologue pair is monoisotopic, while the heavier ion contains a single carbon isotope. The observed abundance ratio is governed by the percentage of carbon atoms lost during the fragmentation and can be described by a hypergeometric distribution. RESULTS: The observed carbon isotopologue abundance ratio (product ion isotopologue pattern) gives reliable information regarding the percentage of carbon atoms lost in the fragmentation process. It therefore facilitates the elucidation of the involved precursor and product ions. Unlike conventional isotopic abundances, the product ion isotopologue pattern is hardly affected by isobaric interferences. Furthermore, the appearance of these pairs greatly aids in cleaning up a 'matrix-contaminated' product ion spectrum. CONCLUSIONS: The product ion isotopologue pattern is a valuable tool for structural elucidation. It increases confidence in results and permits structural elucidations for heavier ions. This tool is also very useful in elucidating the elemental composition of product ions. Such information is highly valued in the field of multi-residue analysis, where the accurate mass of product ions is required for the confirmation process. Copyright © 2016 John Wiley & Sons, Ltd. PMID: 26969920 [PubMed - as supplied by publisher]

Related Articles Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles. J Exp Bot. 2016 Mar 11; Authors: Orf I, Timm S, Bauwe H, Fernie AR, Hagemann M, Kopka J, Nikoloski Z Abstract Photorespiration is a process that is crucial for the survival of oxygenic phototrophs in environments that favour the oxygenation reaction of Rubisco. While photorespiration is conserved among cyanobacteria, algae, and embryophytes, it evolved to different levels of complexity in these phyla. The highest complexity is found in embryophytes, where the pathway involves four cellular compartments and respective transport processes. The complexity of photorespiration in embryophytes raises the question whether a simpler system, such as cyanobacteria, may serve as a model to facilitate our understanding of the common key aspects of photorespiration. In this study, we conducted a meta-analysis of publicly available metabolite profiles from the embryophyte Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 grown under conditions that either activate or suppress photorespiration. The comparative meta-analysis evaluated the similarity of metabolite profiles, the variability of metabolite pools, and the patterns of metabolite ratios. Our results show that the metabolic signature of photorespiration is in part conserved between the compared model organisms under conditions that favour the oxygenation reaction. Therefore, our findings support the claim that cyanobacteria can serve as prokaryotic models of photorespiration in embryophytes. PMID: 26969741 [PubMed - as supplied by publisher]

Related Articles Comparative analysis of volatile oils in the stems and roots of Ephedra sinica via GC-MS-based plant metabolomics. Chin J Nat Med. 2016 Feb;14(2):133-40 Authors: Lv MY, Sun JB, Wang M, Fan HY, Zhang ZJ, Xu FG Abstract With a great difference in therapeutic effects of Mahuang (MH, the stems of Ephedra sinica) and Mahuanggen (MHG, the roots of Ephedra sinica), chemical differences between MH and MHG should be investigated. In the present study, gas chromatography-mass spectrometry (GC-MS)-based plant metabolomics was employed to compare volatile oil profiles of MH and MHG. The antioxidant activities of volatile oils from MH and MHG were also compared. 32 differential chemical markers were identified according to the variable importance in the projection (VIP) value of orthogonal partial least squares discriminant analysis (OPLS-DA) and P value of Mann-Whitney test. Among them, chemical markers of tetramethylpyrazine (TMP) and α-terpineol were quantified. Their contents were much higher in most MH samples compared with MHG. The antioxidant assay demonstrated that MH had significantly higher free radical-scavenging activity than MHG. Although MH and MHG derived from the same medicinal plant, there was much difference in their volatile oil profiles. MH samples had significantly higher content of two reported pharmacologically important chemical markers of TMP and α-terpineol, which may account for their different antioxidant activities. PMID: 26968679 [PubMed - in process]

Alcohol Consumption-Related Metabolites in Relation to Colorectal Cancer and Adenoma: Two Case-Control Studies Using Serum Biomarkers. PLoS One. 2016;11(3):e0150962 Authors: Troche JR, Mayne ST, Freedman ND, Shebl FM, Guertin KA, Cross AJ, Abnet CC Abstract Alcohol is a known carcinogen that may be associated with colorectal cancer. However, most epidemiologic studies assess alcoholic beverage consumption using self-reported data, leading to potential exposure misclassification. Biomarkers of alcohol consumption may provide an alternative, complementary approach that reduces misclassification and incorporates individual differences in alcohol metabolism. Therefore, we evaluated the relationship between previously identified alcohol consumption-related metabolites and colorectal cancer and adenoma using serum metabolomics data from two studies. Data on colorectal cancer were obtained from a nested case-control study of 502 US adults (252 cases, 250 controls) within the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Data on colorectal adenoma were obtained from a case-control study of 197 US adults (120 cases, 77 controls) from the Navy Colon Adenoma Study. Unconditional multivariable logistic regression models were fit to calculate odds ratios (OR) and 95% confidence intervals (CI) for eight alcohol consumption-related metabolites identified in a previous analysis: ethyl glucuronide; 4-androstene-3beta,17beta-diol disulfate 1; 5-alpha-androstan-3beta,17beta-diol disulfate; 16-hydroxypalmitate; bilirubin (E,Z or Z,E); cyclo (-leu-pro); dihomo-linoleate (20:2n6); and palmitoleate (16:1n7). We found no clear association between these alcohol consumption-related metabolites and either endpoint. However, we did observe an inverse association between cyclo (-leu-pro) and colorectal adenoma that was only observed in the highest metabolite quantile (OR 4th vs. 1st Quantile = 0.30, 95% CI: 0.12-0.78; P-trend = 0.047), but no association for colorectal cancer. In conclusion, there were no adverse associations between alcohol consumption-related metabolites and colorectal cancer or adenoma. PMID: 26967509 [PubMed - as supplied by publisher]

Metabolomics profiling in plasma samples from glioma patients correlates with tumor phenotypes. Oncotarget. 2016 Mar 7; Authors: Zhao H, Heimberger AB, Lu Z, Wu X, Hodges TR, Song R, Shen J Abstract BACKGROUND: Tumor-based molecular biomarkers have redefined in the classification gliomas. However, the association of systemic metabolomics with glioma phenotype has not been explored yet. METHODS: In this study, we conducted two-step (discovery and validation) metabolomic profiling in plasma samples from 87 glioma patients. The metabolomics data were tested for correlation with glioma grade (high vs low), glioblastoma (GBM) versus malignant gliomas, and IDH mutation status. RESULTS: Five metabolites, namely uracil, arginine, lactate, cystamine, and ornithine, significantly differed between high- and low-grade glioma patients in both the discovery and validation cohorts. When the discovery and validation cohorts were combined, we identified 29 significant metabolites with 18 remaining significant after adjusting for multiple comparisons. Those 18 significant metabolites separated high- from low-grade glioma patients with 91.1% accuracy. In the pathway analysis, a total of 18 significantly metabolic pathways were identified. Similarly, we identified 2 and 6 metabolites that significantly differed between GBM and non-GBM, and IDH mutation positive and negative patients after multiple comparison adjusting. Those 6 significant metabolites separated IDH1 mutation positive from negative glioma patients with 94.4% accuracy. Three pathways were identified to be associated with IDH mutation status. Within arginine and proline metabolism, levels of intermediate metabolites in creatine pathway were all significantly lower in IDH mutation positive than in negative patients, suggesting an increased activity of creatine pathway in IDH mutation positive tumors. CONCLUSION: Our findings identified metabolites and metabolic pathways that differentiated tumor phenotypes. These may be useful as host biomarker candidates to further help glioma molecular classification. PMID: 26967252 [PubMed - as supplied by publisher]

PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. Biomed Res Int. 2016;2016:2891918 Authors: Kalkhof S, Schildbach S, Blumert C, Horn F, von Bergen M, Labudde D Abstract The functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coimmunoprecipitation or affinity purification with quantitative mass spectrometry. Nevertheless, both methods tend to precipitate a high number of background proteins due to nonspecific interactions. To address this challenge the software Protein-Protein-Interaction-Optimizer (PIPINO) was developed to perform an automated data analysis, to facilitate the selection of bona fide binding partners, and to compare the dynamic of interaction networks. In this study we investigated the STAT1 interaction network and its activation dependent dynamics. Stable isotope labeling by amino acids in cell culture (SILAC) was applied to analyze the STAT1 interactome after streptavidin pull-down of biotagged STAT1 from human embryonic kidney 293T cells with and without activation. Starting from more than 2,000 captured proteins 30 potential STAT1 interaction partners were extracted. Interestingly, more than 50% of these were already reported or predicted to bind STAT1. Furthermore, 16 proteins were found to affect the binding behavior depending on STAT1 phosphorylation such as STAT3 or the importin subunits alpha 1 and alpha 6. PMID: 26966684 [PubMed - in process]

Metabolomic Profiling of Statin Use and Genetic Inhibition of HMG-CoA Reductase. J Am Coll Cardiol. 2016 Mar 15;67(10):1200-10 Authors: Würtz P, Wang Q, Soininen P, Kangas AJ, Fatemifar G, Tynkkynen T, Tiainen M, Perola M, Tillin T, Hughes AD, Mäntyselkä P, Kähönen M, Lehtimäki T, Sattar N, Hingorani AD, Casas JP, Salomaa V, Kivimäki M, Järvelin MR, Davey Smith G, Vanhala M, Lawlor DA, Raitakari OT, Chaturvedi N, Kettunen J, Ala-Korpela M Abstract BACKGROUND: Statins are first-line therapy for cardiovascular disease prevention, but their systemic effects across lipoprotein subclasses, fatty acids, and circulating metabolites remain incompletely characterized. OBJECTIVES: This study sought to determine the molecular effects of statin therapy on multiple metabolic pathways. METHODS: Metabolic profiles based on serum nuclear magnetic resonance metabolomics were quantified at 2 time points in 4 population-based cohorts from the United Kingdom and Finland (N = 5,590; 2.5 to 23.0 years of follow-up). Concentration changes in 80 lipid and metabolite measures during follow-up were compared between 716 individuals who started statin therapy and 4,874 persistent nonusers. To further understand the pharmacological effects of statins, we used Mendelian randomization to assess associations of a genetic variant known to mimic inhibition of HMG-CoA reductase (the intended drug target) with the same lipids and metabolites for 27,914 individuals from 8 population-based cohorts. RESULTS: Starting statin therapy was associated with numerous lipoprotein and fatty acid changes, including substantial lowering of remnant cholesterol (80% relative to low-density lipoprotein cholesterol [LDL-C]), but only modest lowering of triglycerides (25% relative to LDL-C). Among fatty acids, omega-6 levels decreased the most (68% relative to LDL-C); other fatty acids were only modestly affected. No robust changes were observed for circulating amino acids, ketones, or glycolysis-related metabolites. The intricate metabolic changes associated with statin use closely matched the association pattern with rs12916 in the HMGCR gene (R(2) = 0.94, slope 1.00 ± 0.03). CONCLUSIONS: Statin use leads to extensive lipid changes beyond LDL-C and appears efficacious for lowering remnant cholesterol. Metabolomic profiling, however, suggested minimal effects on amino acids. The results exemplify how detailed metabolic characterization of genetic proxies for drug targets can inform indications, pleiotropic effects, and pharmacological mechanisms. PMID: 26965542 [PubMed - in process]

Characterization of chemical-induced sterile inflammation in vitro: application of the model compound ketoconazole in a human hepatic co-culture system. Arch Toxicol. 2016 Mar 10; Authors: Wewering F, Jouy F, Wissenbach DK, Gebauer S, Blüher M, Gebhardt R, Pirow R, von Bergen M, Kalkhof S, Luch A, Zellmer S Abstract Liver injury as a result of a sterile inflammation is closely linked to the activation of immune cells, including macrophages, by damaged hepatocytes. This interaction between immune cells and hepatocytes is as yet not considered in any of the in vitro test systems applied during the generation of new drugs. Here, we established and characterized a novel in vitro co-culture model with two human cell lines, HepG2 and differentiated THP-1. Ketoconazole, an antifungal drug known for its hepatotoxicity, was used as a model compound in the testing of the co-culture. Single cultures of HepG2 and THP-1 cells were studied as controls. Different metabolism patterns of ketoconazole were observed for the single and co-culture incubations as well as for the different cell types. The main metabolite N-deacetyl ketoconazole was found in cell pellets, but not in supernatants of cell cultures. Global proteome analysis showed that the NRF2-mediated stress response and the CXCL8 (IL-8) pathway were induced by ketoconazole treatment under co-culture conditions. The upregulation and ketoconazole-induced secretion of several pro-inflammatory cytokines, including CXCL8, TNF-α and CCL3, was observed in the co-culture system only, but not in single cell cultures. Taking together, we provide evidence that the co-culture model applied might be suitable to serve as tool for the prediction of chemical-induced sterile inflammation in liver tissue in vivo. PMID: 26965496 [PubMed - as supplied by publisher]

Metabolomics Study on the Toxicity of Annona squamosa by Ultraperformance Liquid-Chromatography High-Definition Mass Spectrometry Coupled with Pattern Recognition Approach and Metabolic Pathways Analysis. J Ethnopharmacol. 2016 Mar 7; Authors: Miao YJ, Shi YY, Li FQ, Shan CX, Chen Y, Chen JW, Li X Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Annona squamosa Linn (Annonaceae) is a commonly used and effective traditional Chinese medicine (TCM) especially in the South China. The seeds of Annona squamosa Linn (SAS) have been used as a folk remedy to treat "malignant sores" (cancer) in South of China, but they also have high toxicity on human body. AIM OF THE STUDY: To discover the potential biomarkers in the mice caused by SAS. MATERIALS AND METHODS: We made metabonomics studies on the toxicity of SAS by ultraperformance liquid-chromatography high-definition mass spectrometry coupled with pattern recognition approach and metabolic pathways analysis. RESULTS: The significant difference in metabolic profiles and changes of metabolite biomarkers between the Control group and SAS group were well observed. 11 positive ions and 9 negative ions ((P<0.05)) were indicated based on UFLC-QTOF-HDMS. The metabolic pathways of SAS group are discussed according to the identified endogenous metabolites, and eight metabolic pathways are identified using Kyoto Encyclopedia of Genes and Genomes (KEGG). CONCLUSIONS: The present study demonstrates that metabonomics analysis could greatly facilitate and provide useful information for the further comprehensive understanding of the pharmacological activity and potential toxicity of SAS in the progress of them being designed to a new anti-tumor medicine. PMID: 26965366 [PubMed - as supplied by publisher]