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

Dietary Flavonoid Fisetin Increases Abundance of High-Molecular-Mass Hyaluronan Conferring Resistance to Prostate Oncogenesis.

Fri, 24/06/2016 - 13:55
Dietary Flavonoid Fisetin Increases Abundance of High-Molecular-Mass Hyaluronan Conferring Resistance to Prostate Oncogenesis. Carcinogenesis. 2016 Jun 22; Authors: Lall RK, Syed DN, Khan MI, Adhami VM, Gong Y, Lucey JA, Mukhtar H Abstract We and others have previously shown that fisetin a plant flavonoid, has therapeutic potential against many cancer types. Here, we examined the probable mechanism of its action in prostate cancer (PCa) using a global metabolomics approach. HPLC-ESI-MS analysis of tumor xenografts from fisetin treated animals identified several metabolic targets with hyaluronan (HA) as the most affected. Efficacy of fisetin on HA was then evaluated in-vitro and also in-vivo in the transgenic TRAMP mouse model of PCa. SEC-MALS was performed to analyze the molar mass (Mw) distribution of HA. Fisetin treatment downregulated intracellular and secreted HA levels both in-vitro and in-vivo Fisetin inhibited HA synthesis and degradation enzymes, which led to cessation of HA synthesis and also repressed the degradation of the available high-molecular-mass (HMM)-HA. SEC-MALS analysis of intact HA fragment size revealed that cells and animals have more abundance of HMM-HA and less of low-molecular-mass (LMM)-HA upon fisetin treatment. Elevated HA levels have been shown to be associated with disease progression in certain cancer types. Biological responses triggered by HA mainly depend on the HA polymer length where HMM-HA represses mitogenic signaling and has anti-inflammatory properties while LMM-HA promotes proliferation and inflammation. Similarly, Mw analysis of secreted HA fragment size revealed less HMM-HA is secreted that allowed more HMM-HA to be retained within the cells and tissues. Our findings establish that fisetin is an effective, non-toxic, potent HA synthesis inhibitor, which increases abundance of anti-angiogenic HMM-HA and could be used for the management of PCa. PMID: 27335141 [PubMed - as supplied by publisher]

7-dehydrocholesterol efficiently supports Ret signaling in a mouse model of Smith-Opitz-Lemli syndrome.

Fri, 24/06/2016 - 13:55
7-dehydrocholesterol efficiently supports Ret signaling in a mouse model of Smith-Opitz-Lemli syndrome. Sci Rep. 2016;6:28534 Authors: Gou-Fàbregas M, Macià A, Anerillas C, Vaquero M, Jové M, Jain S, Ribera J, Encinas M Abstract Smith-Lemli-Opitz syndrome (SLOS) is a rare disorder of cholesterol synthesis. Affected individuals exhibit growth failure, intellectual disability and a broad spectrum of developmental malformations. Among them, renal agenesis or hypoplasia, decreased innervation of the gut, and ptosis are consistent with impaired Ret signaling. Ret is a receptor tyrosine kinase that achieves full activity when recruited to lipid rafts. Mice mutant for Ret are born with no kidneys and enteric neurons, and display sympathetic nervous system defects causing ptosis. Since cholesterol is a critical component of lipid rafts, here we tested the hypothesis of whether the cause of the above malformations found in SLOS is defective Ret signaling owing to improper lipid raft composition or function. No defects consistent with decreased Ret signaling were found in newborn Dhcr7(-/-) mice, or in Dhcr7(-/-) mice lacking one copy of Ret. Although kidneys from Dhcr7(-/-) mice showed a mild branching defect in vitro, GDNF was able to support survival and downstream signaling of sympathetic neurons. Consistently, GFRα1 correctly partitioned to lipid rafts in brain tissue. Finally, replacement experiments demonstrated that 7-DHC efficiently supports Ret signaling in vitro. Taken together, our findings do not support a role of Ret signaling in the pathogenesis of SLOS. PMID: 27334845 [PubMed - in process]

Association between plasma endocannabinoids and appetite in hemodialysis patients: A pilot study.

Fri, 24/06/2016 - 13:55
Association between plasma endocannabinoids and appetite in hemodialysis patients: A pilot study. Nutr Res. 2016 Jul;36(7):658-62 Authors: Friedman AN, Kim J, Kaiser S, Pedersen TL, Newman JW, Watkins BA Abstract Uremia-associated anorexia may be related to altered levels of long chain n-6 and n-3 polyunsaturated fatty acid (PUFA) derived circulating endocannabinoids (EC) and EC-like compounds that are known to mediate appetite. Our study's hypothesis was that such molecules are associated with appetite in patients with end-stage renal disease. A cross-sectional observational study was performed in 20 chronic hemodialysis patients (9 females, 11 males) and 10 healthy female controls in whom appetite was assessed using the Simplified Nutritional Appetite Questionnaire (SNAQ) and blood drawn in the fasting (and when applicable) pre-dialysis state. Blood levels of PUFA and EC were also measured. Higher blood levels of the long chain n-6 fatty acid 20:4n6 (arachidonic acid) and lower levels of the long chain n-3 fatty acid 20:5n3 (eicosapentaenoic acid) were observed in female hemodialysis patients compared to controls. No differences were observed between male and female patients. In female study participants strong correlations between specific EC-like compounds and total SNAQ scores were noted, including with the n-6 PUFA derived linoleoyl ethanolamide (L-EA; ρ=-0.60, P<.01) and the n-3 PUFA derived docosahexaenoyl ethanolamide (DH-EA; ρ=0.63, P<.01). The L-EA:DH-EA ratio was most strongly associated with the SNAQ score (ρ=-0.74, P≤.001), and its questions associated with appetite (ρ=-0.69, P≤.01) and satiety (ρ=-0.81, P≤.001). These findings support a link between circulating EC and appetite in hemodialysis patients. PMID: 27333956 [PubMed - in process]

Validated High Resolution Mass Spectrometry-Based Approach for Metabolomic Fingerprinting of the Human Gut Phenotype.

Fri, 24/06/2016 - 13:55
Related Articles Validated High Resolution Mass Spectrometry-Based Approach for Metabolomic Fingerprinting of the Human Gut Phenotype. Anal Chem. 2015 Nov 3;87(21):10927-34 Authors: Vanden Bussche J, Marzorati M, Laukens D, Vanhaecke L Abstract Fecal samples are an obvious choice for metabolomic approaches, since they can be obtained noninvasively and allow one to study the interactions between the gut microbiota and the host. The use of ultrahigh performance liquid chromatography hyphenated to Orbitrap high-resolution mass spectrometry (UHPLC-Orbitrap HRMS) in this field is unique. Hence, this study relied on Orbitrap HRMS to develop and validate a metabolic fingerprinting workflow for human feces and in vitro digestive fluids. After chemometric sample extraction optimization, an aqueous dilution appeared necessary to comply to the dynamic range of the MS. The method was proven "fit-for-purpose" through a validation procedure that monitored endogenous metabolites in quality control samples, which displayed in both matrices an excellent linearity (R(2) > 0.990), recoveries ranging from 93% to 105%, and precision with coefficients of variation (CVs) < 15%. Finally, feces from 10 healthy individuals and 13 patients diagnosed with inflammatory bowel disease were subjected to metabolomic fingerprinting. 9553 ions were detected, as well as differentiating profiles between Crohn's disease and ulcerative colitis by means of (orthogonal) partial least-square analysis ((O)PLS)-DA (discriminate analysis) models. Additionally, samples from the dynamic gastrointestinal tract simulator (SHIME (Simulator of the Human Intestinal Microbial Ecosystem) platform) were analyzed resulting in 6446 and 5010 ions for the proximal and distal colonic samples, respectively. Supplementing SHIME feed with antibiotics resulted in a significant shift (P < 0.05) of 27.7% of the metabolites from the proximal data set and 34.3% for the distal one. As a result, the presented fingerprinting approach provided predictive modeling of the gastrointestinal metabolome in vivo and in vitro, offering a window to reveal disease related biomarkers and potential insight into the mechanisms behind pathologies. PMID: 26451617 [PubMed - indexed for MEDLINE]

metabolomics; +16 new citations

Thu, 23/06/2016 - 13:25
16 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 2016/06/23PubMed comprises more than 24 million 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.

Unchaining NK cell-mediated anticancer immunosurveillance.

Wed, 22/06/2016 - 12:54
Unchaining NK cell-mediated anticancer immunosurveillance. Nat Immunol. 2016 Jun 21;17(7):746-747 Authors: Zitvogel L, Kroemer G PMID: 27327996 [PubMed - as supplied by publisher]

Prevention of breast cancer by RANKL/RANK blockade.

Wed, 22/06/2016 - 12:54
Related Articles Prevention of breast cancer by RANKL/RANK blockade. Cell Res. 2016 Jun 21; Authors: Galluzzi L, Buqué A, Kroemer G Abstract Robust genetic evidence in mice and humans indicates that RANK signaling plays a major role in mammary carcinogenesis driven by BRCA1/BRCA2 mutations. These findings may inaugurate a new era of breast cancer prevention, changing the life of millions of women worldwide. PMID: 27325297 [PubMed - as supplied by publisher]

Probing Cancer Cell Metabolism Using NMR Spectroscopy.

Wed, 22/06/2016 - 12:54
Related Articles Probing Cancer Cell Metabolism Using NMR Spectroscopy. Adv Exp Med Biol. 2016;899:89-111 Authors: Hollinshead KE, Williams DS, Tennant DA, Ludwig C Abstract Altered cellular metabolism is now accepted to be at the core of many diseases including cancer. Over the past 20 years, NMR has become a core technology to study these metabolic perturbations in detail. This chapter reviews current NMR-based methods for steady-state metabolism and, in particular, the use of non-radioactive stable isotope-enriched tracers. Opportunities and challenges for each method, such as 1D (1)H NMR spectroscopy and (13)C carbon-based NMR spectroscopic methods, are discussed. Ultimately, the combination of NMR and mass spectra as orthogonal technologies are required to compensate for the drawbacks of each technique when used singly are discussed. PMID: 27325263 [PubMed - in process]

Gas Chromatography Coupled to Mass Spectrometry (GC-MS) to Study Metabolism in Cultured Cells.

Wed, 22/06/2016 - 12:54
Related Articles Gas Chromatography Coupled to Mass Spectrometry (GC-MS) to Study Metabolism in Cultured Cells. Adv Exp Med Biol. 2016;899:59-88 Authors: Grimm F, Fets L, Anastasiou D Abstract Cancer cells exhibit characteristic patterns of metabolic behaviour that can be exploited for therapeutic purposes. Conditions found within the tumour microenvironment, such as hypoxia and selective nutrient availability, are known to influence the metabolism of cancer and stromal cells. Understanding cancer metabolism requires the use of analytical methods that allow detection and quantification of many metabolites simultaneously. Gas chromatography-mass spectrometry (GC-MS) is a versatile method to quantify metabolite abundance and, in combination with stable isotope labelled compounds, can yield important insights into the activity of metabolic pathways in cancer cells. This chapter provides an overview of the use of GC-MS for metabolic analysis of adherent cancer cells with an emphasis on the technical background that should be taken into consideration when designing and executing GC-MS-based metabolomics experiments. PMID: 27325262 [PubMed - in process]

Glucose Metabolism and AMPK Signaling Regulate Dopaminergic Cell Death Induced by Gene (α-Synuclein)-Environment (Paraquat) Interactions.

Wed, 22/06/2016 - 12:54
Related Articles Glucose Metabolism and AMPK Signaling Regulate Dopaminergic Cell Death Induced by Gene (α-Synuclein)-Environment (Paraquat) Interactions. Mol Neurobiol. 2016 Jun 20; Authors: Anandhan A, Lei S, Levytskyy R, Pappa A, Panayiotidis MI, Cerny RL, Khalimonchuk O, Powers R, Franco R Abstract While environmental exposures are not the single cause of Parkinson's disease (PD), their interaction with genetic alterations is thought to contribute to neuronal dopaminergic degeneration. However, the mechanisms involved in dopaminergic cell death induced by gene-environment interactions remain unclear. In this work, we have revealed for the first time the role of central carbon metabolism and metabolic dysfunction in dopaminergic cell death induced by the paraquat (PQ)-α-synuclein interaction. The toxicity of PQ in dopaminergic N27 cells was significantly reduced by glucose deprivation, inhibition of hexokinase with 2-deoxy-D-glucose (2-DG), or equimolar substitution of glucose with galactose, which evidenced the contribution of glucose metabolism to PQ-induced cell death. PQ also stimulated an increase in glucose uptake, and in the levels of glucose transporter type 4 (GLUT4) and Na(+)-glucose transporters isoform 1 (SGLT1) proteins, but only inhibition of GLUT-like transport with STF-31 or ascorbic acid reduced PQ-induced cell death. Importantly, while autophagy protein 5 (ATG5)/unc-51 like autophagy activating kinase 1 (ULK1)-dependent autophagy protected against PQ toxicity, the inhibitory effect of glucose deprivation on cell death progression was largely independent of autophagy or mammalian target of rapamycin (mTOR) signaling. PQ selectively induced metabolomic alterations and adenosine monophosphate-activated protein kinase (AMPK) activation in the midbrain and striatum of mice chronically treated with PQ. Inhibition of AMPK signaling led to metabolic dysfunction and an enhanced sensitivity of dopaminergic cells to PQ. In addition, activation of AMPK by PQ was prevented by inhibition of the inducible nitric oxide syntase (iNOS) with 1400W, but PQ had no effect on iNOS levels. Overexpression of wild type or A53T mutant α-synuclein stimulated glucose accumulation and PQ toxicity, and this toxic synergism was reduced by inhibition of glucose metabolism/transport and the pentose phosphate pathway (6-aminonicotinamide). These results demonstrate that glucose metabolism and AMPK regulate dopaminergic cell death induced by gene (α-synuclein)-environment (PQ) interactions. PMID: 27324791 [PubMed - as supplied by publisher]

Development of a transplantable glioma tumour model from genetically engineered mice: MRI/MRS/MRSI characterisation.

Wed, 22/06/2016 - 12:54
Related Articles Development of a transplantable glioma tumour model from genetically engineered mice: MRI/MRS/MRSI characterisation. J Neurooncol. 2016 Jun 21; Authors: Ciezka M, Acosta M, Herranz C, Canals JM, Pumarola M, Candiota AP, Arús C Abstract The initial aim of this study was to generate a transplantable glial tumour model of low-intermediate grade by disaggregation of a spontaneous tumour mass from genetically engineered models (GEM). This should result in an increased tumour incidence in comparison to GEM animals. An anaplastic oligoastrocytoma (OA) tumour of World Health Organization (WHO) grade III was obtained from a female GEM mouse with the S100β-v-erbB/inK4a-Arf (+/-) genotype maintained in the C57BL/6 background. The tumour tissue was disaggregated; tumour cells from it were grown in aggregates and stereotactically injected into C57BL/6 mice. Tumour development was followed using Magnetic Resonance Imaging (MRI), while changes in the metabolomics pattern of the masses were evaluated by Magnetic Resonance Spectroscopy/Spectroscopic Imaging (MRS/MRSI). Final tumour grade was evaluated by histopathological analysis. The total number of tumours generated from GEM cells from disaggregated tumour (CDT) was 67 with up to 100 % penetrance, as compared to 16 % in the local GEM model, with an average survival time of 66 ± 55 days, up to 4.3-fold significantly higher than the standard GL261 glioblastoma (GBM) tumour model. Tumours produced by transplantation of cells freshly obtained from disaggregated GEM tumour were diagnosed as WHO grade III anaplastic oligodendroglioma (ODG) and OA, while tumours produced from a previously frozen sample were diagnosed as WHO grade IV GBM. We successfully grew CDT and generated tumours from a grade III GEM glial tumour. Freezing and cell culture protocols produced progression to grade IV GBM, which makes the developed transplantable model qualify as potential secondary GBM model in mice. PMID: 27324642 [PubMed - as supplied by publisher]

Multimode gradient high performance liquid chromatography mass spectrometry method applicable to metabolomics and environmental monitoring.

Wed, 22/06/2016 - 12:54
Related Articles Multimode gradient high performance liquid chromatography mass spectrometry method applicable to metabolomics and environmental monitoring. J Chromatogr A. 2016 Jun 5; Authors: Ammann AA, Suter MJ Abstract Metabolomics or environmental investigations generate samples containing very large numbers of small molecular weight analytes. A single mode chromatographic separation excludes a substantial part of such complex analyte mixtures. For instance, a reversed-phase separation would not retain ionic species, resulting in a correspondingly huge front peak. To address this problem, we used two commercially available mixed-mode ion-exchange reversed-phase columns (WAX-1 and WCX-1) in sequence in a novel multimode separation method. After trapping hydrophobics on a C18-trap in loop position, hydrophilics passing the trap are separated by a simultaneous gradient for HILIC, anion and cation exchange chromatography. This gradient ends in a washout phase with a high percentage of water, the correct starting conditions for a reversed-phase gradient eluting hydrophobics from the trap in a second step of the run. Amino acids (9), organic acids (2), sugars (8), fatty acid derived compounds (11), antioxidants (4), miscellanea (6) and xenobiotics (4) were analyzed. Compounds were separated after a single sample injection during a 50min run. Lipids derived small fatty acids up to a chain length of 12 carbons were also accessible within this run time. PMID: 27324626 [PubMed - as supplied by publisher]

Characterization of the Plasmodium falciparum and P. berghei glycerol 3-phosphate acyltransferase involved in FASII fatty acid utilization in the malaria parasite apicoplast.

Wed, 22/06/2016 - 12:54
Related Articles Characterization of the Plasmodium falciparum and P. berghei glycerol 3-phosphate acyltransferase involved in FASII fatty acid utilization in the malaria parasite apicoplast. Cell Microbiol. 2016 Jun 20; Authors: Shears MJ, MacRae JI, Mollard V, Goodman CD, Sturm A, Orchard LM, Llinás M, McConville MJ, Botté CY, McFadden GI Abstract Malaria parasites can synthesize fatty acids via a type II fatty acid synthesis (FASII) pathway located in their apicoplast. The FASII pathway has been pursued as an anti-malarial drug target, but surprisingly little is known about its role in lipid metabolism. Here we characterize the apicoplast glycerol 3-phosphate acyltransferase that acts immediately downstream of FASII in human (Plasmodium falciparum) and rodent (P. berghei) malaria parasites and investigate how this enzyme contributes to incorporating FASII fatty acids into precursors for membrane lipid synthesis. Apicoplast targeting of the P. falciparum and P. berghei enzymes are confirmed by fusion of the N-terminal targeting sequence to GFP and 3' tagging of the full length protein. Activity of the P. falciparum enzyme is demonstrated by complementation in mutant bacteria, and critical residues in the putative active site identified by site-directed mutagenesis. Genetic disruption of the P. falciparum enzyme demonstrates it is dispensable in blood stage parasites, even in conditions known to induce FASII activity. Disruption of the P. berghei enzyme demonstrates it is dispensable in blood and mosquito stage parasites, and only essential for development in the late liver stage, consistent with the requirement for FASII in rodent models. However, the P. berghei mutant liver stage phenotype is found to only partially phenocopy loss of FASII, suggesting newly made fatty acids can take multiple pathways out of the apicoplast and so giving new insight into the role of FASII and apicoplast glycerol 3-phosphate acyltransferase in malaria parasites. PMID: 27324409 [PubMed - as supplied by publisher]

A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis.

Wed, 22/06/2016 - 12:54
Related Articles A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis. Nat Commun. 2016;7:11933 Authors: Liu Y, Link H, Liu L, Du G, Chen J, Sauer U Abstract Recent advances in genome engineering have further widened the gap between our ability to implement essentially any genetic change and understanding the impact of these changes on cellular function. We lack efficient methods to diagnose limiting steps in engineered pathways. Here, we develop a generally applicable approach to reveal limiting steps within a synthetic pathway. It is based on monitoring metabolite dynamics and simplified kinetic modelling to differentiate between putative causes of limiting product synthesis during the start-up phase of the pathway with near-maximal rates. We examine the synthetic N-acetylglucosamine (GlcNAc) pathway in Bacillus subtilis and find none of the acetyl-, amine- or glucose-moiety precursors to limit synthesis. Our dynamic metabolomics approach predicts an energy-dissipating futile cycle between GlcNAc6P and GlcNAc as the primary problem in the pathway. Deletion of the responsible glucokinase more than doubles GlcNAc productivity by restoring healthy growth of the overproducing strain. PMID: 27324299 [PubMed - in process]

Investigating the early metabolic fingerprint of celiac disease - a prospective approach.

Wed, 22/06/2016 - 12:54
Related Articles Investigating the early metabolic fingerprint of celiac disease - a prospective approach. J Autoimmun. 2016 Jun 17; Authors: Kirchberg FF, Werkstetter KJ, Uhl O, Auricchio R, Castillejo G, Korponay-Szabo IR, Polanco I, Ribes-Koninckx C, Vriezinga SL, Koletzko B, Mearin ML, Hellmuth C Abstract OBJECTIVES AND STUDY: In the development of Celiac Disease (CD) both genetic and environmental factors play a crucial role. The Human Leukocyte Antigen (HLA)-DQ2 and HLA-DQ8 loci are strongly related to the disease and are necessary but not sufficient for the development of CD. Therefore, increasing interest lies in examining the mechanisms of CD onset from the early beginning. Differences in serum and urine metabolic profiles between healthy individuals and CD patients have been reported previously. We aimed to investigate if the metabolic pathways were already altered in young, 4 month old infants, preceding the CD diagnosis. METHODS: Serum samples were available for 230 four month old infants of the PreventCD project, a multicenter, randomized, double-blind, dietary intervention study. All children were positive for HLA-DQ2 and/or HLA-DQ8 and had at least one first-degree relative diagnosed with CD. Amino acids were quantified after derivatization with liquid chromatography - tandem mass spectrometry (MS/MS) and polar lipid concentrations (acylcarnitines, lysophosphatidylcholines, phosphatidylcholines, and sphingomyelins) were determined with direct infusion MS/MS. We investigated the association of the metabolic profile with (1) the development of CD up to the age of 8 years (yes/no), (2) with HLA-risk groups, (3) with the age at CD diagnosis, using linear mixed models and cox proportional hazards models. Gender, intervention group, and age at blood withdrawal were included as potential confounder. RESULTS: By the end of 2014, thirty-three out of the 230 children (14%) were diagnosed with CD according to the ESPGHAN criteria. Median age at diagnosis was 3.4 years (IQR, 2.4-5.2). Testing each metabolite for a difference in the mean between healthy and CD children, we (1) could not identify a discriminant analyte or a pattern pointing towards an altered metabolism (Bonferroni corrected P > 0.05 for all). Metabolite concentrations (2) did not differ across the HLA-risk groups. When investigating the age at diagnosis using (3) survival models, we found no evidence for an association between the metabolic profile and the risk of a later CD diagnosis. CONCLUSION: The metabolic profile at 4 months of age was not predictive for the development of CD up to the age of 8 years. Our results suggest that metabolic pathways reflected in serum are affected only later in life and that the HLA-genotype does not influence the serum metabolic profile in young infants before introduction of solid food. PMID: 27323936 [PubMed - as supplied by publisher]

Analytical pitfalls and challenges in clinical metabolomics.

Wed, 22/06/2016 - 12:54
Related Articles Analytical pitfalls and challenges in clinical metabolomics. Bioanalysis. 2016 Jun 21; Authors: Kohler I, Verhoeven A, Derks RJ, Giera M Abstract Metabolomics-based strategies have become an integral part of modern clinical research, allowing for a better understanding of pathophysiological conditions and disease mechanisms, as well as providing innovative tools for more adequate diagnostic and prognosis approaches. Metabolomics is considered an essential tool in precision medicine, which aims for personalized prevention and tailor-made treatments. Nevertheless, multiple pitfalls may be encountered in clinical metabolomics during the entire workflow, hampering the quality of the data and, thus, the biological interpretation. This review describes the challenges underlying metabolomics-based experiments, discussing step by step the potential pitfalls of the analytical process, including study design, sample collection, storage, as well as preparation, chromatographic and electrophoretic separation, detection and data analysis. Moreover, it offers practical solutions and strategies to tackle these challenges, ensuring the generation of high-quality data. PMID: 27323646 [PubMed - as supplied by publisher]

Single- versus Multiple-Pest Infestation Affects Differently the Biochemistry of Tomato (Solanum lycopersicum 'Ailsa Craig').

Wed, 22/06/2016 - 12:54
Related Articles Single- versus Multiple-Pest Infestation Affects Differently the Biochemistry of Tomato (Solanum lycopersicum 'Ailsa Craig'). J Agric Food Chem. 2015 Nov 25;63(46):10103-11 Authors: Errard A, Ulrichs C, Kühne S, Mewis I, Drungowski M, Schreiner M, Baldermann S Abstract Tomato is susceptible to pest infestations by both spider mites and aphids. The effects of each individual pest on plants are known, whereas multiple-pest infestations have received little interest. We studied the effects of single- versus multiple-pest infestation by Tetranychus urticae and Myzus persicae on tomato biochemistry (Solanum lycopersicum) by combining a metabolomic approach and analyses of carotenoids using UHPLC-ToF-MS and volatiles using GC-MS. Plants responded differently to aphids and mites after 3 weeks of infestation, and a multiple infestation induced a specific metabolite composition in plants. In addition, we showed that volatiles emissions differed between the adaxial and abaxial leaf epidermes and identified compounds emitted particularly in response to a multiple infestation (cyclohexadecane, dodecane, aromadendrene, and β-elemene). Finally, the carotenoid concentrations in leaves and stems were more affected by multiple than single infestations. Our study highlights and discusses the interplay of biotic stressors within the terpenoid metabolism. PMID: 26507319 [PubMed - indexed for MEDLINE]

Activation of surrogate death receptor signaling triggers peroxynitrite-dependent execution of cisplatin-resistant cancer cells.

Wed, 22/06/2016 - 12:54
Related Articles Activation of surrogate death receptor signaling triggers peroxynitrite-dependent execution of cisplatin-resistant cancer cells. Cell Death Dis. 2015;6:e1926 Authors: Seah S, Low IC, Hirpara JL, Sachaphibulkij K, Kroemer G, Brenner C, Pervaiz S Abstract Platinum-based drugs remain as the cornerstone of cancer chemotherapy; however, development of multidrug resistance presents a therapeutic challenge. This study aims at understanding the molecular mechanisms underlying resistance to cisplatin and unraveling surrogate signaling networks that could revert sensitivity to apoptosis stimuli. We made use of three different sets of cell lines, A549 and H2030 non-small-cell lung cancer (NSCLC) and A2780 ovarian cancer cells and their cisplatin-resistant variants. Here we report that cisplatin-resistant cell lines displayed a multidrug-resistant phenotype. Changes in mitochondrial metabolism and defective mitochondrial signaling were unraveled in the resistant cells. More interestingly, a marked increase in sensitivity of the resistant cells to death receptor-induced apoptosis, in particular TRAIL (TNF-related apoptosis-inducing ligand)-mediated execution, was observed. Although this was not associated with an increase in gene transcription, a significant increase in the localization of TRAIL death receptor, DR4, to the lipid raft subdomains of plasma membrane was detected in the resistant variants. Furthermore, exposure of cisplatin-resistant cells to TRAIL resulted in upregulation of inducible nitric oxide synthase (iNOS) and increase in nitric oxide (NO) production that triggered the generation of peroxynitrite (ONOO(-)). Scavenging ONOO(-) rescued cells from TRAIL-induced apoptosis, thereby suggesting a critical role of ONOO(-) in TRAIL-induced execution of cisplatin-resistant cells. Notably, preincubation of cells with TRAIL restored sensitivity of resistant cells to cisplatin. These data provide compelling evidence for employing strategies to trigger death receptor signaling as a second-line treatment for cisplatin-resistant cancers. PMID: 26492363 [PubMed - indexed for MEDLINE]

metabolomics; +21 new citations

Tue, 21/06/2016 - 12:15
21 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 2016/06/21PubMed comprises more than 24 million 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.

Time-resolved NMR metabolomics of plant cells based on a microfluidic chip.

Mon, 20/06/2016 - 14:28
Time-resolved NMR metabolomics of plant cells based on a microfluidic chip. J Plant Physiol. 2016 Jun 10;200:28-34 Authors: Maisch J, Kreppenhofer K, Büchler S, Merle C, Sobich S, Görling B, Luy B, Ahrens R, Guber AE, Nick P Abstract The plant secondary metabolism generates numerous compounds harbouring pharmaceutical activity. In plants, these compounds are typically formed by different and specialised cell types that have to interact constituting a metabolic process chain. This interactivity impedes biotechnological production of secondary compounds, because cell differentiation is suppressed under the conditions of a batch bio-fermenter. We present a novel strategy to address this limitation using a biomimetic approach, where we simulate the situation in a real tissue by a microfluidic chamber system, where plant cells can be integrated into a process flow. We show that walled cells of the plant model tobacco BY-2 can be successfully cultivated in this system and that physiological parameters (such as cell viability, mitotic index and division synchrony) can be preserved over several days. The microfluidic design allows to resolve dynamic changes of specific metabolites over different stages of culture development. These results serve as proof-of-principle that a microfluidic organisation of cultivated plant cells can mimic the metabolic flows in a real plant tissue. PMID: 27318870 [PubMed - as supplied by publisher]

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