Systematic Identification of Conserved Metabolites in GC/MS Data for Metabolomics and Biomarker Discovery

Styczynski, Mark P.; Moxley, Joel F.; Tong, L.; Walther, Jason L.; Jensen, Kyle; Stephanopoulos, Gregory

doi:10.1021/ac0614846

Cited by 227 publications

(172 citation statements)

References 36 publications

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“…This may be due to practical difficulties surrounding sample preparation and data analysis. Our laboratory has previously developed two computational programs to facilitate metabolomic data analysis: SpectConnect for GC-MSbased metabolic profiling (26) and Metran for stable isotopic flux analysis (29). In the present study, we applied these tools for pathway analysis in lipoapoptotic cells and successfully identified phenotype-specific changes.…”

Section: Discussionmentioning

confidence: 98%

Effect of Anaplerotic Fluxes and Amino Acid Availability on Hepatic Lipoapoptosis

Noguchi

Young

Alemán

et al. 2009

Journal of Biological Chemistry

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To identify metabolic pathways involved in hepatic lipoapoptosis, metabolic flux analysis using [U-13 C 5 ]glutamine as an isotopic tracer was applied to quantify phenotypic changes in H4IIEC3 hepatoma cells treated with either palmitate alone (PA-cells) or both palmitate and oleate in combination (PA/OAcells). Our results indicate that palmitate inhibited glycolysis and lactate dehydrogenase fluxes while activating citric acid cycle (CAC) flux and glutamine uptake. This decoupling of glycolysis and CAC fluxes occurred during the period following palmitate exposure but preceding the onset of apoptosis. Oleate co-treatment restored most fluxes to their control levels, resulting in steatotic lipid accumulation while preventing apoptosis. In addition, palmitate strongly increased the cytosolic NAD ؉ / NADH ratio, whereas oleate co-treatment had the opposite effect on cellular redox. We next examined the influence of amino acids on these free fatty acid-induced phenotypic changes. Increased medium amino acids enhanced reactive oxygen species (ROS) generation and apoptosis in PA-cells but not in PA/OAcells. Overloading the medium with non-essential amino acids induced apoptosis, but essential amino acid overloading partially ameliorated apoptosis. Glutamate was the most effective single amino acid in promoting ROS. Amino acid overloading also increased cellular palmitoyl-ceramide; however, ceramide synthesis inhibitors had no effect on measurable indicators of apoptosis. Our results indicate that free fatty acid-induced ROS generation and apoptosis are accompanied by the decoupling of glycolysis and CAC fluxes leading to abnormal cytosolic redox states. Amino acids play a modulatory role in these processes via a mechanism that does not involve ceramide accumulation.Elevated serum free fatty acids (FFAs) 4 cause hepatic apoptosis, which is a prominent feature of non-alcoholic steatohepatitis and correlates with disease severity (1). Previous in vitro studies in Chinese hamster ovary (CHO) cells (2, 3), cardiac myocytes (4, 5), pancreatic ␤-cells (6), breast cancer cells (7), and hepatic cells (8,9) have demonstrated that saturated fatty acids (SFAs) but not monounsaturated fatty acids (MUFAs) induce reactive oxygen species (ROS) generation and apoptosis, whereas MUFAs predominately induce steatosis. An earlier study showed that MUFA co-treatment changed the palmitateinduced phenotype from apoptosis to steatosis by diverting SFAs into triglyceride synthesis and thereby reducing apoptosis in CHO cells (2). Increasing the desaturation of cellular fatty acids by stearoyl-CoA desaturase overexpression had an effect similar to that of oleate co-treatment in MIN6 cells (6).Ceramide accumulation has been considered a primary factor responsible for SFA-induced ROS generation and apoptosis, because ceramide is synthesized de novo from palmitate and serine and also has been shown to activate apoptotic signaling (10, 11). Recent studies, however, have reported that SFAs can induce apoptosis through ROS formation (3) and endoplasm...

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Section: Discussionmentioning

confidence: 98%

Effect of Anaplerotic Fluxes and Amino Acid Availability on Hepatic Lipoapoptosis

Noguchi

Young

Alemán

et al. 2009

Journal of Biological Chemistry

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“…Analyses of GC-MS samples were carried out using Spectconnect (http: //spectconnect.mit.edu/), a novel software program recently developed to reduce noise (54). Although all metabolites could not be identified, we obtained 84 unique metabolite level measurements (52 intracellular measurements and 32 extracellular measurements).…”

Section: Methodsmentioning

confidence: 99%

Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces cerevisiae

Pizarro

Jewett

Nielsen

et al. 2008

Appl Environ Microbiol

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Laboratory strains of Saccharomyces cerevisiae have been widely used as a model for studying eukaryotic cells and mapping the molecular mechanisms of many different human diseases. Industrial wine yeasts, on the other hand, have been selected on the basis of their adaptation to stringent environmental conditions and the organoleptic properties that they confer to wine. Here, we used a two-factor design to study the responses of a standard laboratory strain, CEN.PK113-7D, and an industrial wine yeast strain, EC1118, to growth temperatures of 15°C and 30°C in nitrogen-limited, anaerobic, steady-state chemostat cultures. Physiological characterization revealed that the growth temperature strongly impacted the biomass yield of both strains. Moreover, we found that the wine yeast was better adapted to mobilizing resources for biomass production and that the laboratory yeast exhibited higher fermentation rates. To elucidate mechanistic differences controlling the growth temperature response and underlying adaptive mechanisms between the strains, DNA microarrays and targeted metabolome analysis were used. We identified 1,007 temperature-dependent genes and 473 strain-dependent genes. The transcriptional response was used to identify highly correlated gene expression subnetworks within yeast metabolism. We showed that temperature differences most strongly affect nitrogen metabolism and the heat shock response. A lack of stress response element-mediated gene induction, coupled with reduced trehalose levels, indicated that there was a decreased general stress response at 15°C compared to that at 30°C. Differential responses among strains were centered on sugar uptake, nitrogen metabolism, and expression of genes related to organoleptic properties. Our study provides global insight into how growth temperature affects differential physiological and transcriptional responses in laboratory and wine strains of S. cerevisiae.

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“…It has been found that hundreds of metabolites are present in E. coli (Styczynski et al 2007). However, these metabolites, including benzaldehyde and diacetyl, are abundant in nature.…”

Section: Discussionmentioning

confidence: 99%

Serotonin mediates a learned increase in attraction to high concentrations of benzaldehyde in aged C. elegans

Tsui

Kooy²

2008

Learn. Mem.

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We utilized olfactory-mediated chemotaxis in Caenorhabditis elegans to examine the effect of aging on information processing and animal behavior. Wild-type (N2) young adults (day 4) initially approach and eventually avoid a point source of benzaldehyde. Aged adult animals (day 7) showed a stronger initial approach and a delayed avoidance to benzaldehyde compared with young adults. This delayed avoidance is due to an increased attraction rather than a decreased avoidance to benzaldehyde because (1) aged odr-3 mutants that are defective in odor attraction showed no delayed benzaldehyde avoidance, and (2) the delay in avoidance was also observed with another attractant diacetyl, but not the repellent octanol. Interestingly, the stronger expression of attractive behavior was only observed at benzaldehyde concentrations of 1% or higher. When worms were grown on nonbacterial growth media instead of Escherichia coli, thus removing the contingency between odors released from the food and the food itself, the increase in attraction to benzaldehyde disappeared. The increased attraction recovered after reinitiating the odor-food contingency by returning animals to E. coli food or supplementing axenic media with benzaldehyde. Moreover, serotonin-deficient mutants showed a deficit in the age-enhanced attraction. These results suggest that the increased attraction to benzaldehyde in aged worms is (1) serotonin mediated, (2) specific to high concentration of odorants, and (3) dependent on a learned association of odor metabolites with the presence of food. We propose that associative learning may selectively modify pathways at or downstream from a low-affinity olfactory receptor.Aging is a process of gradual deterioration of physiological function with increase in age. Caenorhabditis elegans exhibit functional declines that are analogous to humans, such as loss of muscle mass and function (Herndon et al. 2002;Evason et al. 2005), making it a good model for the study of different aspects of aging in specific tissues. Moreover, because of its powerful genetic database and a broad range of genetic techniques, C. elegans is widely used as the model for studying the genetics of aging. While most studies of aging in C. elegans focus on easily observable traits such as life span and lipofuscin accumulation (Boehm and Slack 2005;Gerstbrein et al. 2005), few studies have looked at the behavioral consequences of C. elegans aging.One of the behavioral changes that occur with aging is a change in sensory function. In humans, the ability to identify smells peaks between the third and fifth decades of life and declines to the end of life (Doty et al. 1984). Olfactory-mediated chemotaxis in C. elegans requires the integration of sensory and motor function and provides a relatively simple system to study how aging affects olfactory-mediated behaviors. C. elegans can detect and approach or avoid many odorants (Bargmann et al. 1993;Troemel et al. 1995). One of these odorants, benzaldehyde, is sensed by the AWC primary chemosensory neuron (Bargm...

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Systematic Identification of Conserved Metabolites in GC/MS Data for Metabolomics and Biomarker Discovery

Cited by 227 publications

References 36 publications

Effect of Anaplerotic Fluxes and Amino Acid Availability on Hepatic Lipoapoptosis

Effect of Anaplerotic Fluxes and Amino Acid Availability on Hepatic Lipoapoptosis

Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces cerevisiae

Serotonin mediates a learned increase in attraction to high concentrations of benzaldehyde in aged C. elegans

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