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Witkowski M, Nemet I, Li XS, Wilcox J, Ferrell M, Alamri H, Gupta N, Wang Z, Tang WHW, Hazen SL. Xylitol is prothrombotic and associated with cardiovascular risk. Eur Heart J 2024; 45:2439-2452. [PMID: 38842092 DOI: 10.1093/eurheartj/ehae244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/20/2024] [Accepted: 04/07/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND AND AIMS The pathways and metabolites that contribute to residual cardiovascular disease risks are unclear. Low-calorie sweeteners are widely used sugar substitutes in processed foods with presumed health benefits. Many low-calorie sweeteners are sugar alcohols that also are produced endogenously, albeit at levels over 1000-fold lower than observed following consumption as a sugar substitute. METHODS Untargeted metabolomics studies were performed on overnight fasting plasma samples in a discovery cohort (n = 1157) of sequential stable subjects undergoing elective diagnostic cardiac evaluations; subsequent stable isotope dilution liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses were performed on an independent, non-overlapping validation cohort (n = 2149). Complementary isolated human platelet, platelet-rich plasma, whole blood, and animal model studies examined the effect of xylitol on platelet responsiveness and thrombus formation in vivo. Finally, an intervention study was performed to assess the effects of xylitol consumption on platelet function in healthy volunteers (n = 10). RESULTS In initial untargeted metabolomics studies (discovery cohort), circulating levels of a polyol tentatively assigned as xylitol were associated with incident (3-year) major adverse cardiovascular event (MACE) risk. Subsequent stable isotope dilution LC-MS/MS analyses (validation cohort) specific for xylitol (and not its structural isomers) confirmed its association with incident MACE risk [third vs. first tertile adjusted hazard ratio (95% confidence interval), 1.57 (1.12-2.21), P < .01]. Complementary mechanistic studies showed xylitol-enhanced multiple indices of platelet reactivity and in vivo thrombosis formation at levels observed in fasting plasma. In interventional studies, consumption of a xylitol-sweetened drink markedly raised plasma levels and enhanced multiple functional measures of platelet responsiveness in all subjects. CONCLUSIONS Xylitol is associated with incident MACE risk. Moreover, xylitol both enhanced platelet reactivity and thrombosis potential in vivo. Further studies examining the cardiovascular safety of xylitol are warranted.
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Affiliation(s)
- Marco Witkowski
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Ina Nemet
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Xinmin S Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Jennifer Wilcox
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Marc Ferrell
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Hassan Alamri
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Nilaksh Gupta
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Wai Hong Wilson Tang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Stanley L Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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Shaw C, Weimer BC, Gann R, Desai PT, Shah JD. The Yin and Yang of pathogens and probiotics: interplay between Salmonella enterica sv. Typhimurium and Bifidobacterium infantis during co-infection. Front Microbiol 2024; 15:1387498. [PMID: 38812689 PMCID: PMC11133690 DOI: 10.3389/fmicb.2024.1387498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/12/2024] [Indexed: 05/31/2024] Open
Abstract
Probiotic bacteria have been proposed as an alternative to antibiotics for the control of antimicrobial resistant enteric pathogens. The mechanistic details of this approach remain unclear, in part because pathogen reduction appears to be both strain and ecology dependent. Here we tested the ability of five probiotic strains, including some from common probiotic genera Lactobacillus and Bifidobacterium, to reduce binding of Salmonella enterica sv. Typhimurium to epithelial cells in vitro. Bifidobacterium longum subsp. infantis emerged as a promising strain; however, S. Typhimurium infection outcome in epithelial cells was dependent on inoculation order, with B. infantis unable to rescue host cells from preceding or concurrent infection. We further investigated the complex mechanisms underlying this interaction between B. infantis, S. Typhimurium, and epithelial cells using a multi-omics approach that included gene expression and altered metabolism via metabolomics. Incubation with B. infantis repressed apoptotic pathways and induced anti-inflammatory cascades in epithelial cells. In contrast, co-incubation with B. infantis increased in S. Typhimurium the expression of virulence factors, induced anaerobic metabolism, and repressed components of arginine metabolism as well as altering the metabolic profile. Concurrent application of the probiotic and pathogen notably generated metabolic profiles more similar to that of the probiotic alone than to the pathogen, indicating a central role for metabolism in modulating probiotic-pathogen-host interactions. Together these data imply crosstalk via small molecules between the epithelial cells, pathogen and probiotic that consistently demonstrated unique molecular mechanisms specific probiotic/pathogen the individual associations.
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Affiliation(s)
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States
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Yan L, Rust BM, Palmer DG. Time-restricted feeding restores metabolic flexibility in adult mice with excess adiposity. Front Nutr 2024; 11:1340735. [PMID: 38425486 PMCID: PMC10902009 DOI: 10.3389/fnut.2024.1340735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction Obesity is prevalent with the adult population in the United States. Energy-dense diets and erratic eating behavior contribute to obesity. Time-restricted eating is a dietary strategy in humans that has been advanced to reduce the propensity for obesity. We hypothesized that time-restricted feeding (TRF) would improve metabolic flexibility and normalize metabolic function in adult mice with established excess adiposity. Methods Male C57BL/6NHsd mice were initially fed a high-fat diet (HFD) for 12 weeks to establish excess body adiposity, while control mice were fed a normal diet. Then, the HFD-fed mice were assigned to two groups, either ad libitum HFD or TRF of the HFD in the dark phase (12 h) for another 12 weeks. Results and discussion Energy intake and body fat mass were similar in TRF and HFD-fed mice. TRF restored rhythmic oscillations of respiratory exchange ratio (RER), which had been flattened by the HFD, with greater RER amplitude in the dark phase. Insulin sensitivity was improved and plasma cholesterol and hepatic triacylglycerol were decreased by TRF. When compared to HFD, TRF decreased transcription of circadian genes Per1 and Per2 and genes encoding lipid metabolism (Acaca, Fads1, Fads2, Fasn, Scd1, and Srebf1) in liver. Metabolomic analysis showed that TRF created a profile that was distinct from those of mice fed the control diet or HFD, particularly in altered amino acid profiles. These included aminoacyl-tRNA-biosynthesis, glutathione metabolism, and phenylalanine, tyrosine, and tryptophan biosynthesis pathways. In conclusion, TRF improved metabolic function in adult mice with excess adiposity. This improvement was not through a reduction in body fat mass but through the restoration of metabolic flexibility.
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Affiliation(s)
- Lin Yan
- United States Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
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Shi H, Wu X, Zhu Y, Jiang T, Wang Z, Li X, Liu J, Zhang Y, Chen F, Gao J, Xu X, Zhang G, Xiao N, Feng X, Zhang P, Wu Y, Li A, Chen P, Li X. RefMetaPlant: a reference metabolome database for plants across five major phyla. Nucleic Acids Res 2024; 52:D1614-D1628. [PMID: 37953341 PMCID: PMC10767953 DOI: 10.1093/nar/gkad980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC-MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A 'Reference Metabolome Database for Plants' (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like 'LC-MS/MS Query', 'RefMetaBlast' and 'CompoundLibBlast' for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.
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Affiliation(s)
- Han Shi
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueting Wu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Jiang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | | | - Xuetong Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jianju Liu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, China
| | | | - Feng Chen
- Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Jinshan Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xiaoyan Xu
- Core Facility Center, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Peng Zhang
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yongrui Wu
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Aihong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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Sanclemente JL, Rivera-Velez SM, Horohov DW, Dasgupta N, Sanz MG. Plasma metabolome of healthy and Rhodococcus equi-infected foals over time. Equine Vet J 2023; 55:831-842. [PMID: 36273247 DOI: 10.1111/evj.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 09/25/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Foals that develop pulmonary ultrasonographic lesions on Rhodococcus equi (R. equi) endemic farms are treated with antibiotics because those at risk of developing clinical pneumonia (~20%) cannot be recognised early. Candidate biomarkers identified using metabolomics may aid targeted treatment strategies against R. equi. OBJECTIVES (1) To describe how foal ageing affects their plasma metabolome (birth to 8 weeks) and (2) to establish the effects that experimental infection with Rhodococcus equi (R. equi) has on foal metabolome. STUDY DESIGN Experimental study. METHODS Nine healthy newborn foals were experimentally infected with R. equi as described in a previous study. Foals were treated with oral antibiotics if they developed clinical pneumonia (n = 4, clinical group) or remained untreated if they showed no signs of disease (n = 5, subclinical group). A group of unchallenged foals (n = 4) was also included in the study. By the end of the study period (8 weeks), all foals were free of disease. This status was confirmed with transtracheal wash fluid evaluation and culture as well as thoracic ultrasonography. Plasma metabolomics was determined by GC-MS weekly for the study duration (8 weeks). RESULTS Foals' plasma metabolome was altered by ageing (birth to 8 weeks) and experimental infection with R. equi as demonstrated using multivariate statistical analysis. The intensities of 25 and 28 metabolites were altered by ageing and infection (p < 0.05) respectively. Furthermore, 20 metabolites changed by more than 2-fold between clinical and subclinical groups. MAIN LIMITATIONS The number of foals is limited. Foals were experimentally infected with R. equi. CONCLUSIONS Ageing and R. equi infection induced changes in the plasma metabolome of foals. These results provide an initial description of foal's plasma metabolome and serve as background for future identification of R. equi pneumonia biomarkers.
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Affiliation(s)
- Jorge L Sanclemente
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Sol M Rivera-Velez
- Molecular Determinants Core, Johns Hopkins All Children's Hospital, St Petersburg, Florida, USA
| | - David W Horohov
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Clinical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Nairanjana Dasgupta
- Department of Mathematics and Statistics, College of Arts and Sciences, Washington State University, Pullman, Washington, USA
| | - Macarena G Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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Dhillon J, Newman JW, Fiehn O, Ortiz RM. Almond Consumption for 8 Weeks Altered Host and Microbial Metabolism in Comparison to a Control Snack in Young Adults. JOURNAL OF THE AMERICAN NUTRITION ASSOCIATION 2023; 42:242-254. [PMID: 35512761 PMCID: PMC9396742 DOI: 10.1080/07315724.2021.2025168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/10/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Almond consumption can improve cardiometabolic (CM) health. However, the mechanisms underlying those benefits are not well characterized. This study explored the effects of consuming a snack of almonds vs. crackers for 8 weeks on changes in metabolomic profiles in young adults (clinicaltrials.gov ID: NCT03084003). Participants (n = 73, age: 18-19 years, BMI: 18-41 kg/m2) were randomly assigned to consume either almonds (2 oz/d, n = 38) or an isocaloric control snack of graham crackers (325 kcal/d, n = 35) daily for 8 weeks. Blood samples were collected at baseline prior to and at 4 and 8 weeks after the intervention. Metabolite abundances in the serum were quantified by hydrophilic interaction chromatography quadrupole (Q) time-of-flight (TOF) mass spectrometry (MS/MS), gas chromatography (GC) TOF MS, CSH-ESI (electrospray) QTOF MS/MS, and targeted analyses for free PUFAs, total fatty acids, oxylipins and endocannabinoids. Linear mixed model analyses with baseline-adjustment were conducted, and those results were used for enrichment and network analyses. Microbial community pathway predictions from 16S rRNA sequencing of fecal samples was done using PICRUST2. Almond consumption enriched unsaturated triglycerides, unsaturated phosphatidylcholines, saturated and unsaturated lysophosphatidylcholines, tricarboxylic acids, and tocopherol clusters (p < 0.05). Targeted analyses reveal lower levels of omega-3 total fatty acids (TFAs) overall in the almond group compared to the cracker group (p < 0.05). Microbial amino acid biosynthesis, and amino sugar and nucleotide sugar metabolism pathways were also differentially enriched at the end of the intervention (p < 0.05). The study demonstrates the differential effects of almonds on host tocopherol, lipid, and TCA cycle metabolism with potential changes in microbial metabolism, which may interact with host metabolism to facilitate the CM benefits.
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Affiliation(s)
- Jaapna Dhillon
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia
- Department of Molecular and Cell Biology, University of California, Merced
| | - John W. Newman
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis CA, USA
- Department of Nutrition, University of California, Davis
- Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, University of California, Davis
| | - Oliver Fiehn
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis CA, USA
| | - Rudy M. Ortiz
- Department of Molecular and Cell Biology, University of California, Merced
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Yan L, Rust BM, Sundaram S, Bukowski MR. Metabolomic Alterations in Mammary Glands from Pubertal Mice Fed a High-Fat Diet. Nutr Metab Insights 2023; 16:11786388221148858. [PMID: 36744049 PMCID: PMC9893363 DOI: 10.1177/11786388221148858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/14/2022] [Indexed: 02/04/2023] Open
Abstract
Dietary malpractice is a risk factor for obesity. This study tested the hypothesis that consumption of a high-fat diet alters mammary metabolome in pubertal mice. We performed untargeted metabolomic analysis of primary metabolism on mammary glands from pubertal mice fed the AIN93G standard diet or a high-fat diet (HFD) for 3 weeks. We identified 97 metabolites for statistical comparisons. The HFD altered the amino acid metabolism considerably. This included elevated expression of branched-chain amino acids, non-essential amino acids (aspartic acid and glutamic acid), and methionine sulfoxide (oxidized methionine) and an alteration in the aminoacyl-tRNA biosynthesis pathway. Furthermore, elevations of fumaric acid and malic acid (both are citrate cycle intermediates) and glyceric acid (its phosphate derivatives are intermediates of glycolysis) in HFD-fed mice suggest an acceleration of both citrate cycle and glycolysis. Lower expression of glycerol, oleic acid, and palmitoleic acid, as well as decreased mammary expression of genes encoding lipid metabolism (Acaca, Fads1, Fasn, Scd1, and Srebf1) in HFD-fed mice indicate an attenuated lipid metabolism in the presence of adequate dietary fat. In conclusion, consumption of the HFD for 3 weeks alters metabolic profile of pubertal mammary glands. This alteration may affect mammary development and growth in pubertal mice.
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Affiliation(s)
- Lin Yan
- Lin Yan, Lin, USDA-ARS Grand Forks Human
Nutrition Research Center, Grand Forks, ND 58203, USA.
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8
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Yan L, Rust BM, Sundaram S, Picklo MJ, Bukowski MR. Alteration in Plasma Metabolome in High-Fat Diet-Fed Monocyte Chemotactic Protein-1 Knockout Mice Bearing Pulmonary Metastases of Lewis Lung Carcinoma. Nutr Metab Insights 2022; 15:11786388221111126. [PMID: 35959507 PMCID: PMC9358346 DOI: 10.1177/11786388221111126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Both clinical and laboratory studies have shown that monocyte chemotactic protein-1 (MCP-1) is involved in cancer spread. To understand the role of MCP-1 in metabolism in the presence of metastasis, we conducted an untargeted metabolomic analysis of primary metabolism on plasma collected from a study showing that MCP-1 deficiency reduces spontaneous metastasis of Lewis lung carcinoma (LLC) to the lungs in mice fed a high-fat diet (HFD). In a 2 × 2 design, wild-type (WT) or Mcp-1 knockout (Mcp-1 -/-) mice maintained on the AIN93G standard diet or HFD were subcutaneously injected with LLC cells to induce lung metastasis. We identified 87 metabolites for metabolomic analysis from this study. Amino acid metabolism was altered considerably in the presence of LLC metastases with the aminoacyl-tRNA biosynthesis pathways as the leading pathway altered. The HFD modified lipid and energy metabolism, evidenced by lower contents of arachidonic acid, cholesterol, and long-chain saturated fatty acids and higher contents of glucose and pyruvic acid in mice fed the HFD. These findings were supported by network analysis showing alterations in fatty acid synthesis and glycolysis/gluconeogenesis pathways between the 2 diets. Furthermore, elevations of the citrate cycle intermediates (citric acid, fumaric acid, isocitric acid, and succinic acid) and glyceric acid in Mcp-1 -/- mice, regardless of diet, suggest the involvement of MCP-1 in mitochondrial energy metabolism during LLC metastasis. The present study demonstrates that MCP-1 deficiency and the HFD altered plasma metabolome in mice bearing LLC metastases. These findings can be useful in understanding the impact of obesity on prevention and treatment of cancer metastasis.
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Affiliation(s)
- Lin Yan
- U.S. Department of Agriculture, Agricultural
Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND,
USA
| | - Bret M Rust
- U.S. Department of Agriculture, Agricultural
Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND,
USA
| | - Sneha Sundaram
- U.S. Department of Agriculture, Agricultural
Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND,
USA
| | - Matthew J Picklo
- U.S. Department of Agriculture, Agricultural
Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND,
USA
| | - Michael R Bukowski
- U.S. Department of Agriculture, Agricultural
Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND,
USA
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Lilley LM, Sanche S, Moore SC, Salemi MR, Vu D, Iyer S, Hengartner NW, Mukundan H. Methods to capture proteomic and metabolomic signatures from cerebrospinal fluid and serum of healthy individuals. Sci Rep 2022; 12:13339. [PMID: 35922450 PMCID: PMC9349260 DOI: 10.1038/s41598-022-16598-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
Discovery of reliable signatures for the empirical diagnosis of neurological diseases-both infectious and non-infectious-remains unrealized. One of the primary challenges encountered in such studies is the lack of a comprehensive database representative of a signature background that exists in healthy individuals, and against which an aberrant event can be assessed. For neurological insults and injuries, it is important to understand the normal profile in the neuronal (cerebrospinal fluid) and systemic fluids (e.g., blood). Here, we present the first comparative multi-omic human database of signatures derived from a population of 30 individuals (15 males, 15 females, 23-74 years) of serum and cerebrospinal fluid. In addition to empirical signatures, we also assigned common pathways between serum and CSF. Together, our findings provide a cohort against which aberrant signature profiles in individuals with neurological injuries/disease can be assessed-providing a pathway for comprehensive diagnostics and therapeutics discovery.
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Affiliation(s)
- Laura M Lilley
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, 87545, USA
| | - Steven Sanche
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, 87545, USA
| | - Shepard C Moore
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, 87545, USA
| | - Michelle R Salemi
- Genome Center, Proteomics Core Facility, University of California, Davis, CA, 95616, USA
| | - Dung Vu
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, 87545, USA
| | - Srinivas Iyer
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, 87545, USA
| | | | - Harshini Mukundan
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, 87545, USA.
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Aydogan Mathyk B, Piccolo BD, Alvarado F, Shankar K, O'Tierney-Ginn P. Metabolomic signatures of low- and high-adiposity neonates differ based on maternal BMI. Am J Physiol Endocrinol Metab 2022; 322:E540-E550. [PMID: 35466692 PMCID: PMC9169820 DOI: 10.1152/ajpendo.00356.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Maternal obesity [body mass index (BMI) > 30 kg/m2] is associated with greater neonatal adiposity, cord blood (CB) insulin levels, and a proinflammatory phenotype at birth, contributing to risk of future cardiometabolic disease in the offspring. Variation in neonatal adiposity within maternal BMI groups is underappreciated, and it remains unclear whether the metabolic impairments at birth are an outcome of maternal obesity or excess fetal fat accrual. We examined the hypothesis that CB metabolites associated with fetal fat accrual differ between offspring of normal-weight and obese women. Umbilical venous blood was collected at the time of scheduled cesarean delivery from 50 normal-weight women (LE; pregravid BMI = 22.3 ± 1.7 kg/m2) and 50 obese women (OB; BMI = 34.5 ± 3.0 kg/m2). Neonatal adiposity was estimated from flank skinfold thickness. The first (low adiposity, LA) and third (high adiposity, HA) tertiles of neonatal %body fat were used to create four groups: OBLA, OBHA, LELA, and LEHA. CB metabolites were measured via untargeted metabolomics. Broadly, the LA offspring of OB women (OBLA) metabolite signature differed from other groups. Lauric acid (C12:0) was 82-118% higher in OBLA vs. all other groups [false discovery rate (FDR) < 0.01]. Several other fatty acids, including palmitate, stearate, and linoleate, were higher in OBLA vs. OBHA groups. CB metabolites, such as lauric acid, a medium-chain fatty acid that may improve insulin sensitivity, were associated with neonatal adiposity differently between offspring of women with and without obesity. Changes in metabolically active lipids at birth may have long-term consequences for offspring metabolism.NEW & NOTEWORTHY Using untargeted metabolomics in 100 newborns, we found that cord blood metabolite signatures associated with neonatal adiposity differed between offspring of women with and without obesity.
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Affiliation(s)
- Begum Aydogan Mathyk
- Department of Obstetrics and Gynecology, HCA Healthcare/USF Morsani College of Medicine Brandon Regional Hospital, Brandon, Florida
| | - Brian D Piccolo
- United States Department of Agriculture-Agricultural Research Services, Arkansas Children's Nutrition Center, Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Fernanda Alvarado
- Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts
| | - Kartik Shankar
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Cvetkovska M, Zhang X, Vakulenko G, Benzaquen S, Szyszka-Mroz B, Malczewski N, Smith DR, Hüner NPA. A constitutive stress response is a result of low temperature growth in the Antarctic green alga Chlamydomonas sp. UWO241. PLANT, CELL & ENVIRONMENT 2022; 45:156-177. [PMID: 34664276 DOI: 10.1111/pce.14203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
The Antarctic green alga Chlamydomonas sp. UWO241 is an obligate psychrophile that thrives in the cold (4-6°C) but is unable to survive at temperatures ≥18°C. Little is known how exposure to heat affects its physiology or whether it mounts a heat stress response in a manner comparable to mesophiles. Here, we dissect the responses of UWO241 to temperature stress by examining its growth, primary metabolome and transcriptome under steady-state low temperature and heat stress conditions. In comparison with Chlamydomonas reinhardtii, UWO241 constitutively accumulates metabolites and proteins commonly considered as stress markers, including soluble sugars, antioxidants, polyamines, and heat shock proteins to ensure efficient protein folding at low temperatures. We propose that this results from life at extreme conditions. A shift from 4°C to a non-permissive temperature of 24°C alters the UWO241 primary metabolome and transcriptome, but growth of UWO241 at higher permissive temperatures (10 and 15°C) does not provide enhanced heat protection. UWO241 also fails to induce the accumulation of HSPs when exposed to heat, suggesting that it has lost the ability to fine-tune its heat stress response. Our work adds to the growing body of research on temperature stress in psychrophiles, many of which are threatened by climate change.
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Affiliation(s)
- Marina Cvetkovska
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Xi Zhang
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - Galyna Vakulenko
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Samuel Benzaquen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Beth Szyszka-Mroz
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - Nina Malczewski
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - David R Smith
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - Norman P A Hüner
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
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12
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Yan L, Sundaram S, Rust BM, Picklo MJ, Bukowski MR. Mammary Tumorigenesis and Metabolome in Male Adipose Specific Monocyte Chemotactic Protein-1 Deficient MMTV-PyMT Mice Fed a High-Fat Diet. Front Oncol 2021; 11:667843. [PMID: 34568008 PMCID: PMC8458874 DOI: 10.3389/fonc.2021.667843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Male breast cancer, while uncommon, is a highly malignant disease. Monocyte chemotactic protein-1 (MCP-1) is an adipokine; its concentration in adipose tissue is elevated in obesity. This study tested the hypothesis that adipose-derived MCP-1 contributes to male breast cancer. In a 2x2 design, male MMTV-PyMT mice with or without adipose-specific Mcp-1 knockout [designated as Mcp-1-/- or wild-type (WT)] were fed the AIN93G standard diet or a high-fat diet (HFD) for 25 weeks. Mcp-1-/- mice had lower adipose Mcp-1 expression than WT mice. Adipose Mcp-1 deficiency reduced plasma concentrations of MCP-1 in mice fed the HFD compared to their WT counterparts. Mcp-1-/- mice had a longer tumor latency (25.2 weeks vs. 18.0 weeks) and lower tumor incidence (19% vs. 56%), tumor progression (2317% vs. 4792%), and tumor weight (0.23 g vs. 0.64 g) than WT mice. Plasma metabolomics analysis identified 56 metabolites that differed among the four dietary groups, including 22 differed between Mcp-1-/- and WT mice. Pathway and network analyses along with discriminant analysis showed that pathways of amino acid and carbohydrate metabolisms are the most disturbed in MMTV-PyMT mice. In conclusion, adipose-derived MCP-1 contributes to mammary tumorigenesis in male MMTV-PyMT. The potential involvement of adipose-derived MCP-1 in metabolomics warrants further investigation on its role in causal relationships between cancer metabolism and mammary tumorigenesis in this male MMTV-PyMT model.
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Affiliation(s)
- Lin Yan
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Sneha Sundaram
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Bret M Rust
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Matthew J Picklo
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Michael R Bukowski
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
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13
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Smirnov A, Liao Y, Fahy E, Subramaniam S, Du X. ADAP-KDB: A Spectral Knowledgebase for Tracking and Prioritizing Unknown GC-MS Spectra in the NIH's Metabolomics Data Repository. Anal Chem 2021; 93:12213-12220. [PMID: 34455770 DOI: 10.1021/acs.analchem.1c00355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the development of a spectral knowledgebase named ADAP-KDB for tracking and prioritizing unknown gas chromatography-mass spectrometry (GC-MS) spectra in the NIH's Metabolomics Data Repository-a national and international repository for metabolomics data. ADAP-KDB consists of two parts. One part is a computational workflow that preprocesses raw mass spectrometry data and derives consensus mass spectra. The other part is a web portal for users to browse the consensus spectra and match query spectra against them. For each consensus spectrum, the Gini-Simpson diversity index and the p-value from χ2 goodness-of-fit test are calculated to measure its statistical significance, which enables prioritization of unknown mass spectra for subsequent costly compound identification.
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Affiliation(s)
- Aleksandr Smirnov
- University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Yunfei Liao
- University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Eoin Fahy
- University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Shankar Subramaniam
- University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Xiuxia Du
- University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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14
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Liu X, Blaženović I, Contreras AJ, Pham TM, Tabuloc CA, Li YH, Ji J, Fiehn O, Chiu JC. Hexosamine biosynthetic pathway and O-GlcNAc-processing enzymes regulate daily rhythms in protein O-GlcNAcylation. Nat Commun 2021; 12:4173. [PMID: 34234137 PMCID: PMC8263742 DOI: 10.1038/s41467-021-24301-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The integration of circadian and metabolic signals is essential for maintaining robust circadian rhythms and ensuring efficient metabolism and energy use. Using Drosophila as an animal model, we show that cellular protein O-GlcNAcylation exhibits robust 24-hour rhythm and represents a key post-translational mechanism that regulates circadian physiology. We observe strong correlation between protein O-GlcNAcylation rhythms and clock-controlled feeding-fasting cycles, suggesting that O-GlcNAcylation rhythms are primarily driven by nutrient input. Interestingly, daily O-GlcNAcylation rhythms are severely dampened when we subject flies to time-restricted feeding at unnatural feeding time. This suggests the presence of clock-regulated buffering mechanisms that prevent excessive O-GlcNAcylation at non-optimal times of the day-night cycle. We show that this buffering mechanism is mediated by the expression and activity of GFAT, OGT, and OGA, which are regulated through integration of circadian and metabolic signals. Finally, we generate a mathematical model to describe the key factors that regulate daily O-GlcNAcylation rhythm.
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Affiliation(s)
- Xianhui Liu
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA USA
| | - Ivana Blaženović
- grid.27860.3b0000 0004 1936 9684West Coast Metabolomics Center, University of California, Davis, CA USA
| | - Adam J. Contreras
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA USA
| | - Thu M. Pham
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA USA
| | - Christine A. Tabuloc
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA USA
| | - Ying H. Li
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA USA
| | - Jian Ji
- grid.509509.00000 0004 7699 6596School of Food Science, State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, School of Food Science Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu China
| | - Oliver Fiehn
- grid.27860.3b0000 0004 1936 9684West Coast Metabolomics Center, University of California, Davis, CA USA
| | - Joanna C. Chiu
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA USA
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15
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Abstract
Metabolomics is a technology that generates large amounts of data and contributes to obtaining wide and integral explanations of the biochemical state of a living organism. Plants are continuously affected by abiotic stresses such as water scarcity, high temperatures and high salinity, and metabolomics has the potential for elucidating the response-to-stress mechanisms and develop resistance strategies in affected cultivars. This review describes the characteristics of each of the stages of metabolomic studies in plants and the role of metabolomics in the characterization of the response of various plant species to abiotic stresses.
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16
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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17
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Metabolomic Profile of Weaned Pigs Challenged with E. coli and Supplemented with Carbadox or Bacillus subtilis. Metabolites 2021; 11:metabo11020081. [PMID: 33573321 PMCID: PMC7911053 DOI: 10.3390/metabo11020081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 11/17/2022] Open
Abstract
This study explored the metabolomic profiles in ileal mucosa and colon digesta in response to enterotoxigenic Escherichia coli F18 (ETEC) infection and dietary use of probiotics and low-dose antibiotics. Weaned pigs (n = 48, 6.17 ± 0.36 kg body weight) were randomly allotted to one of four treatments. Pigs in the negative control (NC) were fed a basal diet without ETEC challenge, whereas pigs in the positive control (PC), antibiotic, and probiotic groups were fed the basal diet, basal diet supplemented with 50 mg/kg of carbadox, or 500 mg/kg of Bacillus subtilis, respectively, and orally challenged with ETEC F18. All pigs were euthanized at day 21 post-inoculation to collect ileal mucosa and colon digesta for untargeted metabolomic profiling using gas chromatography coupled with time-of-flight mass spectrometry. Multivariate analysis highlighted a more distinct metabolomic profile of ileal mucosa metabolites in NC compared to the ETEC-challenged groups. The relative abundance of 19 metabolites from the ileal mucosa including polyamine, nucleotide, monosaccharides, fatty acids, and organic acids was significantly different between the NC and PC groups (q < 0.1). In colon digesta, differential metabolites including 2-monoolein, lactic acid, and maltose were reduced in the carbadox group compared with the probiotics group. In conclusion, several differential metabolites and metabolic pathways were identified in ileal mucosa, which may suggest an ongoing intestinal mucosal repair in the ileum of ETEC-challenged pigs on day 21 post-inoculation.
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18
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Sanclemente JL, Rivera-Velez SM, Dasgupta N, Horohov DW, Wood PL, Sanz MG. Plasma lipidome of healthy and Rhodococcus equi-infected foals over time. Equine Vet J 2021; 54:121-131. [PMID: 33445210 DOI: 10.1111/evj.13422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Many foals that develop thoracic ultrasonographic lesions as a result of Rhodococcus equi infection heal on their own. However, most of these foals receive antimicrobials because foals at risk of developing clinical pneumonia cannot be identified. Untargeted lipidomics is useful to identify candidate biomarkers. OBJECTIVES (a) To describe the changes that occur in foal lipidomics as a result of ageing (birth to 8 weeks) and (b) To compare these results with those observed in foals after experimental infection with R. equi. STUDY DESIGN Experimental study. METHODS Healthy newborn foals (n = 9) were challenged with R. equi intratracheally the first week of life. Foals were treated with antimicrobials if they developed clinical pneumonia (n = 4, "clinical group") or were closely monitored if they showed no signs of disease (n = 5 "subclinical group"). An unchallenged group (n = 4) was also included. All foals were free of disease (transtracheal wash fluid evaluation and culture as well as thoracic ultrasonography) by 8 weeks of life. Plasma lipidomics was determined by LC-MS weekly for the study duration (8 weeks). RESULTS Both ageing and experimental infection altered the foal's plasma lipidome as demonstrated by multivariate statistical analysis. The intensities of 31 lipids were altered by ageing and 12 by infection (P < .05). Furthermore, nine lipids changed by more than twofold between clinical and subclinical groups. MAIN LIMITATIONS The number of foals is limited. Foals were experimentally challenged with R. equi. CONCLUSIONS Ageing and R. equi infection induced changes in the plasma lipidome of foals. These experimental results provide the background for future work in the discovery of earlier biomarkers of R. equi pneumonia. Early identification of foals at risk of developing clinical pneumonia is key in order to decrease antimicrobial use and development of antimicrobial resistance.
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Affiliation(s)
- Jorge L Sanclemente
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Sol Maiam Rivera-Velez
- Molecular Determinants Core, Johns Hopkins All Children's Hospital, Saint Petersburg, FL, USA
| | - Nairanjana Dasgupta
- Department of Mathematics and Statistics, College of Arts and Sciences, Washington State University, Pullman, WA, USA
| | - David W Horohov
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Clinical Sciences, University of Kentucky, Lexington, KY, USA
| | - Paul L Wood
- Metabolomics Unit, Department of Physiology and Pharmacology, College of Veterinary Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Macarena G Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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19
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Dhillon J, Viscarra JA, Newman JW, Fiehn O, Crocker DE, Ortiz RM. Exogenous GLP-1 stimulates TCA cycle and suppresses gluconeogenesis and ketogenesis in late-fasted northern elephant seals pups. Am J Physiol Regul Integr Comp Physiol 2021; 320:R393-R403. [PMID: 33407018 DOI: 10.1152/ajpregu.00211.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The postweaning fast of northern elephant seal pups is characterized by a lipid-dependent metabolism and associated with a decrease in plasma glucagon-like peptide-1 (GLP-1), insulin, and glucose and increased gluconeogenesis (GNG) and ketogenesis. We have also demonstrated that exogenous GLP-1 infusion increased plasma insulin despite simultaneous increases in cortisol and glucagon, which collectively present contradictory regulatory stimuli of GNG, ketogenesis, and glycolysis. To assess the effects of GLP-1 on metabolism using primary carbon metabolite profiles in late-fasted seal pups, we dose-dependently infused late-fasted seals with low (LDG; 10 pM/kg; n = 3) or high (HDG; 100 pM/kg; n = 4) GLP-1 immediately following a glucose bolus (0.5 g/kg), using glucose without GLP-1 as control (n = 5). Infusions were performed in similarly aged animals 6-8 wk into their postweaning fast. The plasma metabolome was measured from samples collected at five time points just prior to and during the infusions, and network maps constructed to robustly evaluate the effects of GLP-1 on primary carbon metabolism. HDG increased key tricarboxylic acid (TCA) cycle metabolites, and decreased phosphoenolpyruvate and acetoacetate (P < 0.05) suggesting that elevated levels of GLP-1 promote glycolysis and suppress GNG and ketogenesis, which collectively increase glucose clearance. These GLP-1-mediated effects on cellular metabolism help to explain why plasma GLP-1 concentrations decrease naturally in fasting pups as an evolved mechanism to help conserve glucose during the late-fasting period.
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Affiliation(s)
- Jaapna Dhillon
- Department of Molecular & Cell Biology, School of Natural Sciences, University of California, Merced, California.,Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri
| | - Jose A Viscarra
- Department of Molecular & Cell Biology, School of Natural Sciences, University of California, Merced, California.,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California
| | - John W Newman
- Obesity and Metabolism Research Unit, USDA Agricultural Research Service Western Human Nutrition Research Center, University of California, Davis, California.,NIH West Coast Metabolomics Center, University of California, Davis, California
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California, Davis, California
| | - Daniel E Crocker
- Department of Biology, Sonoma State University, Rohnert Park, California
| | - Rudy M Ortiz
- Department of Molecular & Cell Biology, School of Natural Sciences, University of California, Merced, California
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20
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Wanichthanarak K, Boonchai C, Kojonna T, Chadchawan S, Sangwongchai W, Thitisaksakul M. Deciphering rice metabolic flux reprograming under salinity stress via in silico metabolic modeling. Comput Struct Biotechnol J 2020; 18:3555-3566. [PMID: 33304454 PMCID: PMC7708941 DOI: 10.1016/j.csbj.2020.11.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022] Open
Abstract
Rice is one of the most economically important commodities globally. However, rice plants are salt susceptible species in which high salinity can significantly constrain its productivity. Several physiological parameters in adaptation to salt stress have been observed, though changes in metabolic aspects remain to be elucidated. In this study, rice metabolic activities of salt-stressed flag leaf were systematically characterized. Transcriptomics and metabolomics data were combined to identify disturbed pathways, altered metabolites and metabolic hotspots within the rice metabolic network under salt stress condition. Besides, the feasible flux solutions in different context-specific metabolic networks were estimated and compared. Our findings highlighted metabolic reprogramming in primary metabolic pathways, cellular respiration, antioxidant biosynthetic pathways, and phytohormone biosynthetic pathways. Photosynthesis and hexose utilization were among the major disturbed pathways in the stressed flag leaf. Notably, the increased flux distribution of the photorespiratory pathway could contribute to cellular redox control. Predicted flux statuses in several pathways were consistent with the results from transcriptomics, end-point metabolomics, and physiological studies. Our study illustrated that the contextualized genome-scale model together with multi-omics analysis is a powerful approach to unravel the metabolic responses of rice to salinity stress.
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Key Words
- 3-PGA, 3-Phosphoglycerate
- ADH, Arogenate dehydrogenase
- ASA, Ascorbate
- CGS, Cystathionine γ-synthase
- CINV, Cytosolic invertase
- Ci, Intercellular CO2 concentration
- E, Transpiration rate
- GAPDH, Glyceraldehyde-3-phosphate dehydrogenase
- GC-TOF-MS, Gas chromatography time-of-flight mass spectrometry
- GEM, Genome-scale metabolic model
- GLYK, 3-Phosphoglycerate kinase
- GMD, Golm Metabolome Database
- GSH, Glutathione
- GSSG, Glutathione disulfide
- IAA, Indole-3-acetic acid
- IPA, Indolepyruvate
- MAPK, Mitogen-activated protein kinase
- MDH, Malate dehydrogenase
- Metabolic flux analysis
- Metabolic modeling
- Metabolomics
- Multi-omics analysis
- PFK, Phosphofructokinase
- PGK, Phosphoglycerate kinase
- PLS-DA, Partial-Least Squares Discriminant Analysis
- Pn, Net photosynthesis rate
- Rice (Oryza sativa L.)
- SOD, Superoxide dismutase
- Salinity stress
- Systems biology
- TAT, Tyrosine aminotransferase
- Transcriptomics
- gs, Stomatal conductance
- iMAT, Integrative Metabolic Analysis Tool
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Affiliation(s)
- Kwanjeera Wanichthanarak
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chuthamas Boonchai
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Future Innovation and Research in Science and Technology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thammaporn Kojonna
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wichian Sangwongchai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Maysaya Thitisaksakul
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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21
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Lee BM, Lee EM, Kang DJ, Seo JA, Choi HK, Kim YS, Lee DY. Discovery study of integrative metabolic profiles of sesame seeds cultivated in different countries. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Uncovering mechanisms of global ocean change effects on the Dungeness crab (Cancer magister) through metabolomics analysis. Sci Rep 2019; 9:10717. [PMID: 31341175 PMCID: PMC6656712 DOI: 10.1038/s41598-019-46947-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 07/04/2019] [Indexed: 01/22/2023] Open
Abstract
The Dungeness crab is an economically and ecologically important species distributed along the North American Pacific coast. To predict how Dungeness crab may physiologically respond to future global ocean change on a molecular level, we performed untargeted metabolomic approaches on individual Dungeness crab juveniles reared in treatments that mimicked current and projected future pH and dissolved oxygen conditions. We found 94 metabolites and 127 lipids responded in a condition-specific manner, with a greater number of known compounds more strongly responding to low oxygen than low pH exposure. Pathway analysis of these compounds revealed that juveniles may respond to low oxygen through evolutionarily conserved processes including downregulating glutathione biosynthesis and upregulating glycogen storage, and may respond to low pH by increasing ATP production. Most interestingly, we found that the response of juveniles to combined low pH and low oxygen exposure was most similar to the low oxygen exposure response, indicating low oxygen may drive the physiology of juvenile crabs more than pH. Our study elucidates metabolic dynamics that expand our overall understanding of how the species might respond to future ocean conditions and provides a comprehensive dataset that could be used in future ocean acidification response studies.
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23
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Lewis T, Chalise P, Gauldin C, Truog W. Pharmacometabolomics of Respiratory Phenotypic Response to Dexamethasone in Preterm Infants at Risk for Bronchopulmonary Dysplasia. Clin Transl Sci 2019; 12:591-599. [PMID: 31188532 PMCID: PMC6853142 DOI: 10.1111/cts.12659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022] Open
Abstract
A prospective cohort study was performed in preterm infants less than 32 weeks gestation at birth who were treated with dexamethasone for developing or established bronchopulmonary dysplasia (BPD). Respiratory phenotype (Respiratory Severity Score (RSS)), serum, and urine metabolomics were assessed before and after treatment. Ten infants provided nine matched serum and nine matched urine samples. There was a significant decrease in RSS with steroid treatment. Serum gluconic acid had the largest median fold change (140 times decreased, P = 0.008). In metabolite set enrichment analysis, in both serum and urine, the urea cycle, ammonia recycling, and malate-aspartate shuttle pathways were most significantly enriched when comparing pretreatment and post-treatment (P value < 0.05). In regression analyses, 6 serum and 28 urine metabolites were significantly associated with change in RSS. Urine gluconic acid lactone was the most significantly correlated with clinical response (correlational coefficient 0.915). Pharmacometabolomic discovery of drug response biomarkers in preterm infants may allow precision therapeutics in BPD treatment.
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Affiliation(s)
- Tamorah Lewis
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Prabhakar Chalise
- Department of Biostatistics, Kansas University Medical Center, Kansas City, Missouri, USA
| | - Cheri Gauldin
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri Kansas City School of Medicine, Kansas City, Missouri, USA
| | - William Truog
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri Kansas City School of Medicine, Kansas City, Missouri, USA
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24
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Ash JR, Kuenemann MA, Rotroff D, Motsinger-Reif A, Fourches D. Cheminformatics approach to exploring and modeling trait-associated metabolite profiles. J Cheminform 2019; 11:43. [PMID: 31236709 PMCID: PMC6591908 DOI: 10.1186/s13321-019-0366-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/17/2019] [Indexed: 12/17/2022] Open
Abstract
Developing predictive and transparent approaches to the analysis of metabolite profiles across patient cohorts is of critical importance for understanding the events that trigger or modulate traits of interest (e.g., disease progression, drug metabolism, chemical risk assessment). However, metabolites’ chemical structures are still rarely used in the statistical modeling workflows that establish these trait-metabolite relationships. Herein, we present a novel cheminformatics-based approach capable of identifying predictive, interpretable, and reproducible trait-metabolite relationships. As a proof-of-concept, we utilize a previously published case study consisting of metabolite profiles from non-small-cell lung cancer (NSCLC) adenocarcinoma patients and healthy controls. By characterizing each structurally annotated metabolite using both computed molecular descriptors and patient metabolite concentration profiles, we show that these complementary features enhance the identification and understanding of key metabolites associated with cancer. Ultimately, we built multi-metabolite classification models for assessing patients’ cancer status using specific groups of metabolites identified based on high structural similarity through chemical clustering. We subsequently performed a metabolic pathway enrichment analysis to identify potential mechanistic relationships between metabolites and NSCLC adenocarcinoma. This cheminformatics-inspired approach relies on the metabolites’ structural features and chemical properties to provide critical information about metabolite-trait associations. This method could ultimately facilitate biological understanding and advance research based on metabolomics data, especially with respect to the identification of novel biomarkers. ![]()
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Affiliation(s)
- Jeremy R Ash
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Melaine A Kuenemann
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Daniel Rotroff
- Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Denis Fourches
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA. .,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
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25
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Rivera-Velez SM, Broughton-Neiswanger LE, Suarez MA, Slovak JE, Hwang JK, Navas J, Leung AWS, Piñeyro PE, Villarino NF. Understanding the effect of repeated administration of meloxicam on feline renal cortex and medulla: A lipidomics and metabolomics approach. J Vet Pharmacol Ther 2019; 42:476-486. [PMID: 31190341 DOI: 10.1111/jvp.12788] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022]
Abstract
Repeated administration of meloxicam can cause kidney damage in cats by mechanisms that remain unclear. Metabolomics and lipidomics are powerful, noninvasive approaches used to investigate tissue response to drug exposure. Thus, the objective of this study was to assess the effects of meloxicam on the feline kidney using untargeted metabolomics and lipidomics approaches. Female young-adult purpose-breed cats were allocated into the control (n = 4) and meloxicam (n = 4) groups. Cats in the control and meloxicam groups were treated daily with saline and meloxicam at 0.3 mg/kg subcutaneously for 17 days, respectively. Renal cortices and medullas were collected at the end of the treatment period. Random forest and metabolic pathway analyses were used to identify metabolites that discriminate meloxicam-treated from saline-treated cats and to identify disturbed metabolic pathways in renal tissue. Our results revealed that the repeated administration of meloxicam to cats altered the kidney metabolome and lipidome and suggest that at least 40 metabolic pathways were altered in the renal cortex and medulla. These metabolic pathways included lipid, amino acid, carbohydrate, nucleotide and energy metabolisms, and metabolism of cofactors and vitamins. This is the first study using a pharmacometabonomics approach for studying the molecular effects of meloxicam on feline kidneys.
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Affiliation(s)
- Sol M Rivera-Velez
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Liam E Broughton-Neiswanger
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Martin A Suarez
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Jennifer E Slovak
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Julianne K Hwang
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Jinna Navas
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Amy W S Leung
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Pablo E Piñeyro
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Nicolas F Villarino
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington
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26
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Alternative outlets for sustaining photosynthetic electron transport during dark-to-light transitions. Proc Natl Acad Sci U S A 2019; 116:11518-11527. [PMID: 31101712 PMCID: PMC6561286 DOI: 10.1073/pnas.1903185116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Most forms of life on Earth cannot exist without photosynthesis. Our food and atmosphere depend on it. To obtain high photosynthetic yields, light energy must be efficiently coupled to the fixation of CO2 into organic molecules. Suboptimal environmental conditions can severely impact the conversion of light energy to biomass and lead to reactive oxygen production, which in turn can cause cellular damage and loss of productivity. Hence, plants, algae, and photosynthetic bacteria have evolved a network of alternative outlets to sustain the flow of photosynthetically derived electrons. Our work is focused on the nature and integration of these outlets, which will inform a rational engineering of crop plants and algae to optimize photosynthesis and meet the increased global demand for food. Environmental stresses dramatically impact the balance between the production of photosynthetically derived energetic electrons and Calvin–Benson–Bassham cycle (CBBC) activity; an imbalance promotes accumulation of reactive oxygen species and causes cell damage. Hence, photosynthetic organisms have developed several strategies to route electrons toward alternative outlets that allow for storage or harmless dissipation of their energy. In this work, we explore the activities of three essential outlets associated with Chlamydomonas reinhardtii photosynthetic electron transport: (i) reduction of O2 to H2O through flavodiiron proteins (FLVs) and (ii) plastid terminal oxidases (PTOX) and (iii) the synthesis of starch. Real-time measurements of O2 exchange have demonstrated that FLVs immediately engage during dark-to-light transitions, allowing electron transport when the CBBC is not fully activated. Under these conditions, we quantified maximal FLV activity and its overall capacity to direct photosynthetic electrons toward O2 reduction. However, when starch synthesis is compromised, a greater proportion of the electrons is directed toward O2 reduction through both the FLVs and PTOX, suggesting an important role for starch synthesis in priming/regulating CBBC and electron transport. Moreover, partitioning energized electrons between sustainable (starch; energetic electrons are recaptured) and nonsustainable (H2O; energetic electrons are not recaptured) outlets is part of the energy management strategy of photosynthetic organisms that allows them to cope with the fluctuating conditions encountered in nature. Finally, unmasking the repertoire and control of such energetic reactions offers new directions for rational redesign and optimization of photosynthesis to satisfy global demands for food and other resources.
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27
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Park SJ, Kim JK, Kim HH, Yoon BA, Ji DY, Lee CW, Kim HJ, Kim KH, Shin HY, Park SJ, Lee DY. Integrative metabolomics reveals unique metabolic traits in Guillain-Barré Syndrome and its variants. Sci Rep 2019; 9:1077. [PMID: 30705347 PMCID: PMC6355784 DOI: 10.1038/s41598-018-37572-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
Guillain-Barré syndrome (GBS) is an acute fatal progressive disease caused by autoimmune mechanism mainly affecting peripheral nervous system. Although the syndrome is clinically sub-classified into several variants, specific biomarker and exact pathomechanism of each subtypes are not well elucidated yet. In current study, integrative metabolomic and lipidomic profiles were acquisitioned from cerebrospinal fluid samples of 86 GBS from three variants and 20 disease controls. And the data were systematically compared to our previous result on inflammatory demyelination disorders of central nervous system (IDDs) and healthy controls. Primary metabolite profiles revealed unique metabolic traits in which 9 and 7 compounds were specifically changed in GBS and IDD, respectively. Next, the biomarker panel with 10 primary metabolites showed a fairly good discrimination power among 3 GBS subtypes, healthy controls, and disease controls (AUCs ranged 0.849-0.999). The robustness of the biomarker panel was vigorously validated by multi-step statistical evaluation. Subsequent lipidomics revealed GBS variant-specific alteration where the significant elevations of lyso-phosphatidylcholines and sphingomyelins were unique to AIDP (acute inflammatory demyelinating polyneuropathy) and AMAN (acute motor axonal neuropathy), respectively. And metabolome-wide multivariate correlation analysis identified potential clinical association between GBS disability scale (Hughes score) and CSF lipids (monoacylglycerols, and sphingomyelins). Finally, Bayesian network analysis of covarianced structures of primary metabolites and lipids proposed metabolic hub and potential biochemical linkage associated with the pathology.
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Affiliation(s)
- Soo Jin Park
- The Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul, 02707, Republic of Korea
| | - Jong Kuk Kim
- Department of Neurology, Peripheral Neuropathy Research Center, Dong-A University College of Medicine, Busan, 49315, Republic of Korea
| | - Hyun-Hwi Kim
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea
| | - Byeol-A Yoon
- Department of Neurology, Peripheral Neuropathy Research Center, Dong-A University College of Medicine, Busan, 49315, Republic of Korea
| | - Dong Yoon Ji
- The Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul, 02707, Republic of Korea
| | - Chang-Wan Lee
- The Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul, 02707, Republic of Korea
| | - Ho Jin Kim
- The Department of Neurology, Research Institute and Hospital of the National Cancer Center, Goyang, Republic of Korea
| | - Kyoung Heon Kim
- The Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea.
| | - Do Yup Lee
- The Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul, 02707, Republic of Korea.
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28
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La Frano MR, Fahrmann JF, Grapov D, Pedersen TL, Newman JW, Fiehn O, Underwood MA, Mestan K, Steinhorn RH, Wedgwood S. Umbilical cord blood metabolomics reveal distinct signatures of dyslipidemia prior to bronchopulmonary dysplasia and pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol 2018; 315:L870-L881. [PMID: 30113229 PMCID: PMC6295510 DOI: 10.1152/ajplung.00283.2017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/31/2018] [Accepted: 08/15/2018] [Indexed: 01/27/2023] Open
Abstract
Pulmonary hypertension (PH) is a common consequence of bronchopulmonary dysplasia (BPD) and remains a primary contributor to increased morbidity and mortality among preterm infants. Unfortunately, at the present time, there are no reliable early predictive markers for BPD-associated PH. Considering its health consequences, understanding in utero perturbations that lead to the development of BPD and BPD-associated PH and identifying early predictive markers is of utmost importance. As part of the discovery phase, we applied a multiplatform metabolomics approach consisting of untargeted and targeted methodologies to screen for metabolic perturbations in umbilical cord blood (UCB) plasma from preterm infants that did ( n = 21; cases) or did not ( n = 21; controls) develop subsequent PH. A total of 1,656 features were detected, of which 407 were annotated by metabolite structures. PH-associated metabolic perturbations were characterized by reductions in major choline-containing phospholipids, such as phosphatidylcholines and sphingomyelins, indicating altered lipid metabolism. The reduction in UCB abundances of major choline-containing phospholipids was confirmed in an independent validation cohort consisting of UCB plasmas from 10 cases and 10 controls matched for gestational age and BPD status. Subanalyses in the discovery cohort indicated that elevations in the oxylipins PGE1, PGE2, PGF2a, 9- and 13-HOTE, 9- and 13-HODE, and 9- and 13-KODE were positively associated with BPD presence and severity. This expansive evaluation of cord blood plasma identifies compounds reflecting dyslipidemia and suggests altered metabolite provision associated with metabolic immaturity that differentiate subjects, both by BPD severity and PH development.
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Affiliation(s)
- Michael R La Frano
- West Coast Metabolomics Center, University of California, Davis Genome Center, University of California , Davis, California
- Department of Nutrition, University of California , Davis, California
- Department of Food Science and Nutrition, California Polytechnic State University , San Luis Obispo, California
| | - Johannes F Fahrmann
- West Coast Metabolomics Center, University of California, Davis Genome Center, University of California , Davis, California
- Department of Clinical Cancer Prevention, University of Texas M. D. Anderson Cancer Center , Houston, Texas
| | | | - Theresa L Pedersen
- Obesity and Metabolism Research Unit, United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center , Davis, California
| | - John W Newman
- West Coast Metabolomics Center, University of California, Davis Genome Center, University of California , Davis, California
- Department of Nutrition, University of California , Davis, California
- Obesity and Metabolism Research Unit, United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center , Davis, California
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis Genome Center, University of California , Davis, California
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi-Arabia
| | - Mark A Underwood
- Department of Pediatrics, University of California, Davis Medical Center , Sacramento, California
| | - Karen Mestan
- Department of Pediatrics, Division of Neonatology, Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | - Robin H Steinhorn
- Department of Pediatrics, Children's National Medical Center, George Washington University , Washington, District of Columbia
| | - Stephen Wedgwood
- Department of Pediatrics, University of California, Davis Medical Center , Sacramento, California
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29
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Intararuchikul T, Teerapattarakan N, Rodsiri R, Tantisira M, Wohlgemuth G, Fiehn O, Tansawat R. Effects of Centella asiatica extract on antioxidant status and liver metabolome of rotenone-treated rats using GC-MS. Biomed Chromatogr 2018; 33:e4395. [PMID: 30242859 DOI: 10.1002/bmc.4395] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 01/10/2023]
Abstract
Centella asiatica has been used as a culinary vegetable or medicinal herb. In this study, the hepatoprotective effect of the standardized extract of C. asiatica (ECa233) in rotenone-treated rats was examined using a GC-MS-based metabolomic approach. ECa233 contains >80% triterpenoids with a ratio of madecassoside to asiaticoside of 1.5(±0.5):1. Rats were randomly divided into three groups (with six rats/group): sham negative control, rotenone positive control and the ECa233 test group. Rats in the ECa233 group received 10 mg/kg ECa233 orally for 20 days, followed by 2.5 mg/kg intraperitoneal rotenone injection to induce toxicity before being sacrificed. Metabolomic analysis showed that supplementation of ECa233 protected rat liver against rotenone toxicity. Pipecolinic acid was one of the most important metabolites; its level was decreased in the rotenone group as compared with the control. Supplementation with ECa233 before administration of rotenone raised pipecolinic acid to levels intermediate between controls and rotenone alone. The metabolomics approach also helped discover a possible new genuine epimetabolite in the present work. Antioxidant tests revealed that ECa233 inhibited lipid peroxidation and increased catalase activities in liver tissue.
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Affiliation(s)
- Thidarat Intararuchikul
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Narudol Teerapattarakan
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Ratchanee Rodsiri
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Mayuree Tantisira
- Faculty of Pharmaceutical Sciences, Burapha University, Chonburi, Thailand
| | - Gert Wohlgemuth
- NIH West Coast Metabolomics Center, University of California Davis, CA, USA
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, CA, USA.,Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rossarin Tansawat
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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30
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Potent Attractant for Root-Knot Nematodes in Exudates from Seedling Root Tips of Two Host Species. Sci Rep 2018; 8:10847. [PMID: 30022095 PMCID: PMC6052019 DOI: 10.1038/s41598-018-29165-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 07/06/2018] [Indexed: 11/24/2022] Open
Abstract
Root-knot nematodes (RKN; Meloidogyne spp.) can parasitize over 2,000 plant species and are generally considered to be the most agriculturally damaging group of plant-parasitic nematodes worldwide. Infective juveniles (J2) are non-feeding and must locate and invade a host before their reserves are depleted. However, what attracts J2 to appropriate root entry sites is not known. An aim of this research is to identify semiochemicals that attract RKN to roots. J2 of the three RKN species tested are highly attracted to root tips of both tomato and Medicago truncatula. For both hosts, mutants defective in ethylene signaling were found to be more attractive than those of wild type. We determined that cell-free exudates collected from tomato and M. truncatula seedling root tips were highly attractive to M. javanica J2. Using a pluronic gel-based microassay to monitor chemical fractionation, we determined that for both plant species the active component fractionated similarly and had a mass of ~400 based on size-exclusion chromatography. This characterization is a first step toward identification of a potent and specific attractant from host roots that attracts RKN. Such a compound is potentially a valuable tool for developing novel and safe control strategies.
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31
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Sheng L, Jena PK, Liu HX, Hu Y, Nagar N, Bronner DN, Settles ML, Bäumler AJ, Wan YJY. Obesity treatment by epigallocatechin-3-gallate-regulated bile acid signaling and its enriched Akkermansia muciniphila. FASEB J 2018; 32:fj201800370R. [PMID: 29882708 PMCID: PMC6219838 DOI: 10.1096/fj.201800370r] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/14/2018] [Indexed: 12/21/2022]
Abstract
Dysregulated bile acid (BA) synthesis is accompanied by dysbiosis, leading to compromised metabolism. This study analyzes the effect of epigallocatechin-3-gallate (EGCG) on diet-induced obesity through regulation of BA signaling and gut microbiota. The data revealed that EGCG effectively reduced diet-increased obesity, visceral fat, and insulin resistance. Gene profiling data showed that EGCG had a significant impact on regulating genes implicated in fatty acid uptake, adipogenesis, and metabolism in the adipose tissue. In addition, metabolomics analysis revealed that EGCG altered the lipid and sugar metabolic pathways. In the intestine, EGCG reduced the FXR agonist chenodeoxycholic acid, as well as the FXR-regulated pathway, suggesting intestinal FXR deactivation. However, in the liver, EGCG increased the concentration of FXR and TGR-5 agonists and their regulated signaling. Furthermore, our data suggested that EGCG activated Takeda G protein receptor (TGR)-5 based on increased GLP-1 release and elevated serum PYY level. EGCG and antibiotics had distinct antibacterial effects. They also differentially altered body weight and BA composition. EGCG, but not antibiotics, increased Verrucomicrobiaceae, under which EGCG promoted intestinal bloom of Akkermansia muciniphila. Excitingly, A. muciniphila was as effective as EGCG in treating diet-induced obesity. Together, EGCG shifts gut microbiota and regulates BA signaling thereby having a metabolic beneficial effect.-Sheng, L., Jena, P. K., Liu, H.-X., Hu, Y., Nagar, N., Bronner, D. N., Settles, M. L., Bäumler, A. J. Wan, Y.-J. Y. Obesity treatment by epigallocatechin-3-gallate-regulated bile acid signaling and its enriched Akkermansia muciniphila.
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Affiliation(s)
- Lili Sheng
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Prasant Kumar Jena
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Hui-Xin Liu
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Ying Hu
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Nidhi Nagar
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Denise N. Bronner
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Matthew L. Settles
- Bioinformatics Core Facility in the Genome Center, University of California, Davis, Davis, California, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Yu-Jui Yvonne Wan
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
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32
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Morris JK, Piccolo BD, Shankar K, Thyfault JP, Adams SH. The serum metabolomics signature of type 2 diabetes is obscured in Alzheimer's disease. Am J Physiol Endocrinol Metab 2018; 314:E584-E596. [PMID: 29351484 PMCID: PMC6032067 DOI: 10.1152/ajpendo.00377.2017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/07/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022]
Abstract
There is evidence for systemic metabolic impairment in Alzheimer's disease (AD), and type 2 diabetes (T2D) increases AD risk. Although studies analyzing blood metabolomics signatures have shown differences between cognitively healthy (CH) and AD subjects, these signatures have not been compared with individuals with T2D. We utilized untargeted analysis platforms (primary metabolism and complex lipids) to characterize the serum metabolome of 126 overnight-fasted elderly subjects classified into four groups based upon AD status (CH or AD) and T2D status [nondiabetic (ND) or T2D]. Cognitive diagnosis groups were a priori weighted equally with T2D subjects. We hypothesized that AD subjects would display a metabolic profile similar to cognitively normal elderly individuals with T2D. However, partial least squares-discriminant analysis (PLS-DA) modeling resulted in poor classification across the four groups (<50% classification accuracy of test subjects). Binary classification of AD vs. CH was poor, but binary classification of T2D vs. ND was good, providing >79.5% and >76.9% classification accuracy for held-out samples using primary metabolism and complex lipids, respectively. When modeling was limited to CH subjects, T2D discrimination improved for the primary metabolism platform (>89.5%) and remained accurate for complex lipids (>73% accuracy). Greater abundances of glucose, fatty acids (C20:2), and phosphatidylcholines and lower abundances of glycine, maleimide, octanol, and tryptophan, cholesterol esters, phosphatidylcholines, and sphingomyelins were identified in CH subjects with T2D relative to those without T2D. In contrast, T2D was not accurately discriminated within AD subjects. Results herein suggest that AD may obscure the typical metabolic phenotype of T2D.
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Affiliation(s)
- Jill K Morris
- University of Kansas Department of Neurology, University of Kansas Alzheimer's Disease Center , Kansas City, Kansas
- University of Kansas Alzheimer's Disease Center, Fairway, Kansas
| | - Brian D Piccolo
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Kartik Shankar
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - John P Thyfault
- University of Kansas Department of Neurology, University of Kansas Alzheimer's Disease Center , Kansas City, Kansas
- University of Kansas Alzheimer's Disease Center, Fairway, Kansas
- University of Kansas Department of Molecular and Integrative Physiology , Kansas City, Kansas
- Kansas City Veterans Affairs Medical Center , Kansas City, Missouri
| | - Sean H Adams
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Sciences , Little Rock, Arkansas
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33
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Misra BB, Upadhayay RP, Cox LA, Olivier M. Optimized GC-MS metabolomics for the analysis of kidney tissue metabolites. Metabolomics 2018; 14:75. [PMID: 30830353 DOI: 10.1007/s11306-018-1373-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/15/2018] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Metabolomics is a promising approach for discovery of relevant biomarkers in cells, tissues, organs, and biofluids for disease identification and prediction. The field has mostly relied on blood-based biofluids (serum, plasma, urine) as non-invasive sources of samples as surrogates of tissue or organ-specific conditions. However, the tissue specificity of metabolites pose challenges in translating blood metabolic profiles to organ-specific pathophysiological changes, and require further downstream analysis of the metabolites. OBJECTIVES As part of this project, we aim to develop and optimize an efficient extraction protocol for the analysis of kidney tissue metabolites representative of key primate metabolic pathways. METHODS Kidney cortex and medulla tissues of a baboon were homogenized and extracted using eight different extraction protocols including methanol/water, dichloromethane/methanol, pure methanol, pure water, water/methanol/chloroform, methanol/chloroform, methanol/acetonitrile/water, and acetonitrile/isopropanol/water. The extracts were analyzed by a two-dimensional gas chromatography time-of-flight mass-spectrometer (2D GC-ToF-MS) platform after methoximation and silylation. RESULTS Our analysis quantified 110 shared metabolites in kidney cortex and medulla tissues from hundreds of metabolites found among the eight different solvent extractions spanning low to high polarities. The results revealed that medulla is metabolically richer compared to the cortex. Dichloromethane and methanol mixture (3:1) yielded highest number of metabolites across both the tissue types. Depending on the metabolites of interest, tissue type, and the biological question, different solvents can be used to extract specific groups of metabolites. CONCLUSION This investigation provides insights into selection of extraction solvents for detection of classes of metabolites in renal cortex and medulla, which is fundamentally important for identification of prognostic and diagnostic metabolic kidney biomarkers for future therapeutic applications.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
| | - Ram P Upadhayay
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
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Rivera-Vélez SM, Villarino NF. Feline urine metabolomic signature: characterization of low-molecular-weight substances in urine from domestic cats. J Feline Med Surg 2018; 20:155-163. [PMID: 28367722 PMCID: PMC11129257 DOI: 10.1177/1098612x17701010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Objectives This aim of this study was to characterize the composition and content of the feline urine metabolome. Methods Eight healthy domestic cats were acclimated at least 10 days before starting the study. Urine samples (~2 ml) were collected by ultrasound-guided cystocentesis. Samples were centrifuged at 1000 × g for 8 mins, and the supernatant was analyzed by gas chromatography/time-of-flight mass spectrometery. The urine metabolome was characterized using an untargeted metabolomics approach. Results Three hundred and eighteen metabolites were detected in the urine of the eight cats. These molecules are key components of at least 100 metabolic pathways. Feline urine appears to be dominated by carbohydrates, carbohydrate conjugates, organic acid and derivatives, and amino acids and analogs. The five most abundant molecules were phenaceturic acid, hippuric acid, pseudouridine phosphate and 3-(4-hydroxyphenyl) propionic acid. Conclusions and relevance This study is the first to characterize the feline urine metabolome. The results of this study revealed the presence of multiple low-molecular-weight substances that were not known to be present in feline urine. As expected, the origin of the metabolites detected in urine was diverse, including endogenous compounds and molecules biosynthesized by microbes. Also, the diet seemed to have had a relevant role on the urine metabolome. Further exploration of the urine metabolic phenotype will open a window for discovering unknown, or poorly understood, metabolic pathways. In turn, this will advance our understanding of feline biology and lead to new insights in feline physiology, nutrition and medicine.
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Affiliation(s)
- Sol-Maiam Rivera-Vélez
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Nicolas F Villarino
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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Zaini PA, Nascimento R, Gouran H, Cantu D, Chakraborty S, Phu M, Goulart LR, Dandekar AM. Molecular Profiling of Pierce's Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection. FRONTIERS IN PLANT SCIENCE 2018; 9:771. [PMID: 29937771 PMCID: PMC6002507 DOI: 10.3389/fpls.2018.00771] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/18/2018] [Indexed: 05/19/2023]
Abstract
Pierce's disease is a major threat to grapevines caused by the bacterium Xylella fastidiosa. Although devoid of a type 3 secretion system commonly employed by bacterial pathogens to deliver effectors inside host cells, this pathogen is able to influence host parenchymal cells from the xylem lumen by secreting a battery of hydrolytic enzymes. Defining the cellular and biochemical changes induced during disease can foster the development of novel therapeutic strategies aimed at reducing the pathogen fitness and increasing plant health. To this end, we investigated the transcriptional, proteomic, and metabolomic responses of diseased Vitis vinifera compared to healthy plants. We found that several antioxidant strategies were induced, including the accumulation of gamma-aminobutyric acid (GABA) and polyamine metabolism, as well as iron and copper chelation, but these were insufficient to protect the plant from chronic oxidative stress and disease symptom development. Notable upregulation of phytoalexins, pathogenesis-related proteins, and various aromatic acid metabolites was part of the host responses observed. Moreover, upregulation of various cell wall modification enzymes followed the proliferation of the pathogen within xylem vessels, consistent with the intensive thickening of vessels' secondary walls observed by magnetic resonance imaging. By interpreting the molecular profile changes taking place in symptomatic tissues, we report a set of molecular markers that can be further explored to aid in disease detection, breeding for resistance, and developing therapeutics.
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Affiliation(s)
- Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Rafael Nascimento
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - Hossein Gouran
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - My Phu
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Luiz R. Goulart
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- *Correspondence: Abhaya M. Dandekar,
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Lai Z, Tsugawa H, Wohlgemuth G, Mehta S, Mueller M, Zheng Y, Ogiwara A, Meissen J, Showalter M, Takeuchi K, Kind T, Beal P, Arita M, Fiehn O. Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nat Methods 2018; 15:53-56. [PMID: 29176591 PMCID: PMC6358022 DOI: 10.1038/nmeth.4512] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/26/2017] [Indexed: 12/31/2022]
Abstract
Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives.
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Affiliation(s)
- Zijuan Lai
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
- Department of Chemistry, UC Davis, Davis, California USA
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa,
Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa,
Japan
| | - Gert Wohlgemuth
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Sajjan Mehta
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Matthew Mueller
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Yuxuan Zheng
- Department of Chemistry, UC Davis, Davis, California USA
| | | | - John Meissen
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Megan Showalter
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Kohei Takeuchi
- Perfume Development Research Laboratory, Kao Corporation, Sumida,
Tokyo, Japan
| | - Tobias Kind
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Peter Beal
- Department of Chemistry, UC Davis, Davis, California USA
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa,
Japan
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi
Arabia
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37
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Lowe-Power TM, Hendrich CG, von Roepenack-Lahaye E, Li B, Wu D, Mitra R, Dalsing BL, Ricca P, Naidoo J, Cook D, Jancewicz A, Masson P, Thomma B, Lahaye T, Michael AJ, Allen C. Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease. Environ Microbiol 2017; 20:1330-1349. [PMID: 29215193 DOI: 10.1111/1462-2920.14020] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/29/2017] [Accepted: 12/03/2017] [Indexed: 12/20/2022]
Abstract
Ralstonia solanacearum thrives in plant xylem vessels and causes bacterial wilt disease despite the low nutrient content of xylem sap. We found that R. solanacearum manipulates its host to increase nutrients in tomato xylem sap, enabling it to grow better in sap from infected plants than in sap from healthy plants. Untargeted GC/MS metabolomics identified 22 metabolites enriched in R. solanacearum-infected sap. Eight of these could serve as sole carbon or nitrogen sources for R. solanacearum. Putrescine, a polyamine that is not a sole carbon or nitrogen source for R. solanacearum, was enriched 76-fold to 37 µM in R. solanacearum-infected sap. R. solanacearum synthesized putrescine via a SpeC ornithine decarboxylase. A ΔspeC mutant required ≥ 15 µM exogenous putrescine to grow and could not grow alone in xylem even when plants were treated with putrescine. However, co-inoculation with wildtype rescued ΔspeC growth, indicating R. solanacearum produced and exported putrescine to xylem sap. Intriguingly, treating plants with putrescine before inoculation accelerated wilt symptom development and R. solanacearum growth and systemic spread. Xylem putrescine concentration was unchanged in putrescine-treated plants, so the exogenous putrescine likely accelerated disease indirectly by affecting host physiology. These results indicate that putrescine is a pathogen-produced virulence metabolite.
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Affiliation(s)
- Tiffany M Lowe-Power
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Connor G Hendrich
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Edda von Roepenack-Lahaye
- Leibniz Institute of Plant Biochemistry, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Universität Tübingen, Tübingen, Germany
| | - Bin Li
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dousheng Wu
- Leibniz Institute of Plant Biochemistry, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Universität Tübingen, Tübingen, Germany
| | - Raka Mitra
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Beth L Dalsing
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Patrizia Ricca
- Leibniz Institute of Plant Biochemistry, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Universität Tübingen, Tübingen, Germany
| | - Jacinth Naidoo
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David Cook
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Amy Jancewicz
- Department of Genetics, University of Wisconsin, Madison, Madison, WI 53706, USA
| | - Patrick Masson
- Department of Genetics, University of Wisconsin, Madison, Madison, WI 53706, USA
| | - Bart Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Thomas Lahaye
- Leibniz Institute of Plant Biochemistry, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Universität Tübingen, Tübingen, Germany
| | - Anthony J Michael
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706, USA
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Lai Z, Kind T, Fiehn O. Using Accurate Mass Gas Chromatography-Mass Spectrometry with the MINE Database for Epimetabolite Annotation. Anal Chem 2017; 89:10171-10180. [PMID: 28876899 PMCID: PMC8168919 DOI: 10.1021/acs.analchem.7b01134] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mass spectrometry-based untargeted metabolomics often detects statistically significant metabolites that cannot be readily identified. Without defined chemical structure, interpretation of the biochemical relevance is not feasible. Epimetabolites are produced from canonical metabolites by defined enzymatic reactions and may represent a large fraction of the structurally unidentified metabolome. We here present a systematic workflow for annotating unknown epimetabolites using high resolution gas chromatography-accurate mass spectrometry with multiple ionization techniques and stable isotope labeled derivatization methods. We first determine elemental formulas, which are then used to query the "metabolic in-silico expansion" database (MINE DB) to obtain possible molecular structures that are predicted by enzyme promiscuity from canonical pathways. Accurate mass fragmentation rules are combined with in silico spectra prediction programs CFM-ID and MS-FINDER to derive the best candidates. We validated the workflow by correctly identifying 10 methylated nucleosides and 6 methylated amino acids. We then employed this strategy to annotate eight unknown compounds from cancer studies and other biological systems.
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Affiliation(s)
- Zijuan Lai
- West Coast Metabolomics Center, UC Davis, Davis, California 95616, United States
| | - Tobias Kind
- West Coast Metabolomics Center, UC Davis, Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis, Davis, California 95616, United States
- Department of Biochemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Tu LN, Showalter MR, Cajka T, Fan S, Pillai VV, Fiehn O, Selvaraj V. Metabolomic characteristics of cholesterol-induced non-obese nonalcoholic fatty liver disease in mice. Sci Rep 2017; 7:6120. [PMID: 28733574 PMCID: PMC5522413 DOI: 10.1038/s41598-017-05040-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 05/30/2017] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) in non-obese patients remains a clinical condition with unclear etiology and pathogenesis. Using a metabolomics approach in a mouse model that recapitulates almost all the characteristic features of non-obese NAFLD, we aimed to advance mechanistic understanding of this disorder. Mice fed high fat, high cholesterol, cholate (HFHCC) diet for three weeks consistently developed hepatic pathology similar to NAFLD and nonalcoholic steatohepatitis (NASH) without changes to body weight or fat pad weights. Gas- and liquid chromatography/mass spectrometry-based profiling of lipidomic and primary metabolism changes in the liver and plasma revealed that systemic mechanisms leading to steatosis and hepatitis in this non-obese NAFLD model were driven by a combination of effects directed by elevated free cholesterol, cholesterol esters and cholic acid, and associated changes to metabolism of sphingomyelins and phosphatidylcholines. These results demonstrate that mechanisms underlying cholesterol-induced non-obese NAFLD are distinct from NAFLD occurring as a consequence of metabolic syndrome. In addition, this investigation provides one of the first metabolite reference profiles for interpreting effects of dietary and hepatic cholesterol in human non-obese NAFLD/NASH patients.
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Affiliation(s)
- Lan N Tu
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Megan R Showalter
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, 95616, USA
| | - Tomas Cajka
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, 95616, USA
| | - Sili Fan
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, 95616, USA
| | - Viju V Pillai
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, 95616, USA
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vimal Selvaraj
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
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Matsuo T, Tsugawa H, Miyagawa H, Fukusaki E. Integrated Strategy for Unknown EI-MS Identification Using Quality Control Calibration Curve, Multivariate Analysis, EI-MS Spectral Database, and Retention Index Prediction. Anal Chem 2017; 89:6766-6773. [PMID: 28520403 DOI: 10.1021/acs.analchem.7b01010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Compound identification using unknown electron ionization (EI) mass spectra in gas chromatography coupled with mass spectrometry (GC-MS) is challenging in untargeted metabolomics, natural product chemistry, or exposome research. While the total count of EI-MS records included in publicly or commercially available databases is over 900 000, efficient use of this huge database has not been achieved in metabolomics. Therefore, we proposed a "four-step" strategy for the identification of biologically significant metabolites using an integrated cheminformatics approach: (i) quality control calibration curve to reduce background noise, (ii) variable selection by hypothesis testing in principal component analysis for the efficient selection of target peaks, (iii) searching the EI-MS spectral database, and (iv) retention index (RI) filtering in combination with RI predictions. In this study, the new MS-FINDER spectral search engine was developed and utilized for searching EI-MS databases using mass spectral similarity with the evaluation of false discovery rate. Moreover, in silico derivatization software, MetaboloDerivatizer, was developed to calculate the chemical properties of derivative compounds, and all retention indexes in EI-MS databases were predicted using a simple mathematical model. The strategy was showcased in the identification of three novel metabolites (butane-1,2,3-triol, 3-deoxyglucosone, and palatinitol) in Chinese medicine Senkyu for quality assessment, as validated using authentic standard compounds. All tools and curated public EI-MS databases are freely available in the 'Computational MS-based metabolomics' section of the RIKEN PRIMe Web site ( http://prime.psc.riken.jp ).
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Affiliation(s)
- Teruko Matsuo
- Department of Biotechnology, Graduate School of Engineering, Osaka University , 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Tsugawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University , 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University , 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Zheng H, Powell JE, Steele MI, Dietrich C, Moran NA. Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Proc Natl Acad Sci U S A 2017; 114:4775-4780. [PMID: 28420790 PMCID: PMC5422775 DOI: 10.1073/pnas.1701819114] [Citation(s) in RCA: 339] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Social bees harbor a simple and specialized microbiota that is spatially organized into different gut compartments. Recent results on the potential involvement of bee gut communities in pathogen protection and nutritional function have drawn attention to the impact of the microbiota on bee health. However, the contributions of gut microbiota to host physiology have yet to be investigated. Here we show that the gut microbiota promotes weight gain of both whole body and the gut in individual honey bees. This effect is likely mediated by changes in host vitellogenin, insulin signaling, and gustatory response. We found that microbial metabolism markedly reduces gut pH and redox potential through the production of short-chain fatty acids and that the bacteria adjacent to the gut wall form an oxygen gradient within the intestine. The short-chain fatty acid profile contributed by dominant gut species was confirmed in vitro. Furthermore, metabolomic analyses revealed that the gut community has striking impacts on the metabolic profiles of the gut compartments and the hemolymph, suggesting that gut bacteria degrade plant polymers from pollen and that the resulting metabolites contribute to host nutrition. Our results demonstrate how microbial metabolism affects bee growth, hormonal signaling, behavior, and gut physicochemical conditions. These findings indicate that the bee gut microbiota has basic roles similar to those found in some other animals and thus provides a model in studies of host-microbe interactions.
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Affiliation(s)
- Hao Zheng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712;
| | - J Elijah Powell
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Margaret I Steele
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Carsten Dietrich
- Strategy and Innovation Technology Center, Siemens Healthcare GmbH, 91052 Erlangen, Germany
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712;
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Wanichthanarak K, Fan S, Grapov D, Barupal DK, Fiehn O. Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. PLoS One 2017; 12:e0171046. [PMID: 28141874 PMCID: PMC5283729 DOI: 10.1371/journal.pone.0171046] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/13/2017] [Indexed: 01/22/2023] Open
Abstract
Similar to genomic and proteomic platforms, metabolomic data acquisition and analysis is becoming a routine approach for investigating biological systems. However, computational approaches for metabolomic data analysis and integration are still maturing. Metabox is a bioinformatics toolbox for deep phenotyping analytics that combines data processing, statistical analysis, functional analysis and integrative exploration of metabolomic data within proteomic and transcriptomic contexts. With the number of options provided in each analysis module, it also supports data analysis of other 'omic' families. The toolbox is an R-based web application, and it is freely available at http://kwanjeeraw.github.io/metabox/ under the GPL-3 license.
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Affiliation(s)
- Kwanjeera Wanichthanarak
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, California, United States of America
| | - Sili Fan
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, California, United States of America
| | - Dmitry Grapov
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, California, United States of America
| | - Dinesh Kumar Barupal
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, California, United States of America
| | - Oliver Fiehn
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, California, United States of America
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Fahrmann JF, Grapov D, DeFelice BC, Taylor S, Kim K, Kelly K, Wikoff WR, Pass H, Rom WN, Fiehn O, Miyamoto S. Serum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer. Cancer Biomark 2017; 16:609-17. [PMID: 27002763 DOI: 10.3233/cbm-160602] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Recent computed tomography (CT) screening trials showed that it is effective for early detection of lung cancer, but were plagued by high false positive rates. Additional blood biomarker tests designed to complement CT screening and reduce false positive rates are highly desirable. OBJECTIVE Identify blood-based metabolite biomarkers for diagnosing lung cancer. MEHTODS Serum samples from subjects participating in a CT screening trial were analyzed using untargeted GC-TOFMS and HILIC-qTOFMS-based metabolomics. Samples were acquired prior to diagnosis (pre-diagnostic, n= 17), at-diagnosis (n= 25) and post-diagnosis (n= 19) of lung cancer and from subjects with benign nodules (n= 29). RESULTS Univariate analysis identified 40, 102 and 30 features which were significantly different between subjects with malignant (pre-, at- and post-diagnosis) solitary pulmonary nodules (SPNs) and benign SPNs, respectively. Ten metabolites were consistently different between subjects presenting malignant (pre- and at-diagnosis) or benign SPNs. Three of these 10 metabolites were phosphatidylethanolamines (PE) suggesting alterations in lipid metabolism. Accuracies of 77%, 83% and 78% in the pre-diagnosis group and 69%, 71% and 67% in the at-diagnosis group were determined for PE(34:2), PE(36:2) and PE(38:4), respectively. CONCLUSIONS This study demonstrates evidence of early metabolic alterations that can possibly distinguish malignant from benign SPNs. Further studies in larger pools of samples are warranted.
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Affiliation(s)
| | | | - Brian C DeFelice
- University of California, Davis Genome Center, Davis, California, CA, USA
| | - Sandra Taylor
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, California, CA, USA
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, California, CA, USA
| | - Karen Kelly
- Division of Hematology and Oncology, Department of Internal Medicine, School of Medicine, University of California, Davis Medical Center, Sacramento, CA, USA
| | - William R Wikoff
- University of California, Davis Genome Center, Davis, California, CA, USA
| | - Harvey Pass
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Langone Medical Center, New York University, New York, NY, USA
| | - William N Rom
- Division of Pulmonary, Critical Care, and Sleep, NYU School of Medicine, New York, NY, USA
| | - Oliver Fiehn
- University of California, Davis Genome Center, Davis, California, CA, USA.,Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi-Arabia
| | - Suzanne Miyamoto
- Division of Hematology and Oncology, Department of Internal Medicine, School of Medicine, University of California, Davis Medical Center, Sacramento, CA, USA
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Computational Strategies for Biological Interpretation of Metabolomics Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:191-206. [PMID: 28132181 DOI: 10.1007/978-3-319-47656-8_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biological interpretation of metabolomics data relies on two basic steps: metabolite identification and functional analysis. These two steps need to be applied in a coordinated manner to enable effective data understanding. The focus of this chapter is to introduce the main computational concepts and workflows during this process. After a general overview of the field, three sections will be presented: the first section will introduce the main computational methods and bioinformatics tools for metabolite identification using spectra from common analytical platforms; the second section will focus on introducing major bioinformatics approaches for functional enrichment analysis of metabolomics data; and the last section will discuss the three main workflows in current metabolomics studies, including the chemometrics approach, the metabolic profiling approach and the more recent chemo-enrichment analysis approach. The chapter ends with summary and future perspectives on computational metabolomics.
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Liu Y, Chen L, Wu G, Feng H, Zhang G, Shen Q, Zhang R. Identification of Root-Secreted Compounds Involved in the Communication Between Cucumber, the Beneficial Bacillus amyloliquefaciens, and the Soil-Borne Pathogen Fusarium oxysporum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:53-62. [PMID: 27937752 DOI: 10.1094/mpmi-07-16-0131-r] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Colonization of plant growth-promoting rhizobacteria (PGPR) is critical for exerting their beneficial effects on the plant. Root exudation is a major factor influencing the colonization of both PGPR and soil-borne pathogens within the root system. However, the tripartite interaction of PGPR, plant roots, and soil-borne pathogens is poorly understood. We screened root exudates for signals that mediate tripartite interactions in the rhizosphere. In a split-root system, we found that root colonization of PGPR strain Bacillus amyloliquefaciens SQR9 on cucumber root was significantly enhanced by preinoculation with SQR9 or the soil-borne pathogen Fusarium oxysporum f. sp. cucumerinum, whereas root colonization of F. oxysporum f. sp. cucumerinum was reduced upon preinoculation with SQR9 or F. oxysporum f. sp. cucumerinum. Root exudates from cucumbers preinoculated with SQR9 or F. oxysporum f. sp. cucumerinum were analyzed and 109 compounds were identified. Correlation analysis highlighted eight compounds that significantly correlated with root colonization of SQR9 or F. oxysporum f. sp. cucumerinum. After performing colonization experiments with these chemicals, raffinose and tryptophan were shown to positively affect the root colonization of F. oxysporum f. sp. cucumerinum and SQR9, respectively. These results indicate that cucumber roots colonized by F. oxysporum f. sp. cucumerinum or SQR9 increase root secretion of tryptophan to strengthen further colonization of SQR9. In contrast, these colonized cucumber roots reduce raffinose secretion to inhibit root colonization of F. oxysporum f. sp. cucumerinum.
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Affiliation(s)
- Yunpeng Liu
- 1 Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; and
| | - Lin Chen
- 2 Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Gengwei Wu
- 2 Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Haichao Feng
- 2 Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Guishan Zhang
- 1 Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; and
| | - Qirong Shen
- 2 Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Ruifu Zhang
- 1 Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; and
- 2 Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, P.R. China
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46
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Kieffer DA, Piccolo BD, Marco ML, Kim EB, Goodson ML, Keenan MJ, Dunn TN, Knudsen KEB, Adams SH, Martin RJ. Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria. J Nutr 2016; 146:2445-2460. [PMID: 27798344 DOI: 10.3945/jn.116.238923] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/11/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Enzyme-treated wheat bran (ETWB) contains a fermentable dietary fiber previously shown to decrease liver triglycerides (TGs) and modify the gut microbiome in mice. It is not clear which mechanisms explain how ETWB feeding affects hepatic metabolism, but factors (i.e., xenometabolites) associated with specific microbes may be involved. OBJECTIVE The objective of this study was to characterize ETWB-driven shifts in the cecal microbiome and to identify correlates between microbial changes and diet-related differences in liver metabolism in diet-induced obese mice that typically display steatosis. METHODS Five-week-old male C57BL/6J mice fed a 45%-lard-based fat diet supplemented with ETWB (20% wt:wt) or rapidly digestible starch (control) (n = 15/group) for 10 wk were characterized by using a multi-omics approach. Multivariate statistical analysis was used to identify variables that were strong discriminators between the ETWB and control groups. RESULTS Body weight and liver TGs were decreased by ETWB feeding (by 10% and 25%, respectively; P < 0.001), and an index of liver reactive oxygen species was increased (by 29%; P < 0.01). The cecal microbiome showed an increase in Bacteroidetes (by 42%; P < 0.05) and a decrease in Firmicutes (by 16%; P < 0.05). Metabolites that were strong discriminators between the ETWB and control groups included decreased liver antioxidants (glutathione and α-tocopherol); decreased liver carbohydrate metabolites, including glucose; lower hepatic arachidonic acid; and increased liver and plasma β-hydroxybutyrate. Liver transcriptomics revealed key metabolic pathways affected by ETWB, especially those related to lipid metabolism and some fed- or fasting-regulated genes. CONCLUSIONS Together, these changes indicate that dietary fibers such as ETWB regulate hepatic metabolism concurrently with specific gut bacteria community shifts in C57BL/6J mice. It is proposed that these changes may elicit gut-derived signals that reach the liver via enterohepatic circulation, ultimately affecting host liver metabolism in a manner that mimics, in part, the fasting state.
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Affiliation(s)
- Dorothy A Kieffer
- Graduate Group in Nutritional Biology and.,Department of Nutrition.,Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
| | - Brian D Piccolo
- Arkansas Children's Nutrition Center and.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | | | - Eun Bae Kim
- Food Science and Technology Department, and.,Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | | | | | - Tamara N Dunn
- Graduate Group in Nutritional Biology and.,Department of Nutrition.,Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
| | | | - Sean H Adams
- Graduate Group in Nutritional Biology and .,Department of Nutrition.,Arkansas Children's Nutrition Center and.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Roy J Martin
- Graduate Group in Nutritional Biology and .,Department of Nutrition.,Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
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47
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Albrecht U, Fiehn O, Bowman KD. Metabolic variations in different citrus rootstock cultivars associated with different responses to Huanglongbing. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:33-44. [PMID: 27236226 DOI: 10.1016/j.plaphy.2016.05.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 05/03/2023]
Abstract
Huanglongbing (HLB) is one of the most destructive bacterial diseases of citrus. No resistant cultivars have been identified, although tolerance has been observed in the genus Poncirus and some of its hybrids with Citrus that are commonly used as rootstocks. In this study we exploited this tolerance by comparing five different tolerant hybrids with a cultivar that shows pronounced HLB sensitivity to discern potential contributing metabolic factors. Whole leaves of infected and non-infected greenhouse-grown seedlings were extracted and subjected to untargeted GC-TOF MS based metabolomics. After BinBase data filtering, 342 (experiment 1) and 650 (experiment 2) unique metabolites were quantified, of which 122 and 195, respectively, were assigned by chemical structures. The number of metabolites found to be differently regulated in the infected state compared with the non-infected state varied between the cultivars and was largest (166) in the susceptible cultivar Cleopatra mandarin (Citrus reticulata) and lowest (3) in the tolerant cultivars US-897 (C. reticulata 'Cleopatra' × Poncirus trifoliata) and US-942 (C. reticulata 'Sunki' × P. trifoliata) from experiment 2. Tolerance to HLB did not appear to be associated with accumulation of higher amounts of protective metabolites in response to infection. Many metabolites were found in higher concentrations in the tolerant cultivars compared with susceptible Cleopatra mandarin and may play important roles in conferring tolerance to HLB. Lower availability of specific sugars necessary for survival of the pathogen may also be a contributing factor in the decreased disease severity observed for these cultivars.
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Affiliation(s)
- Ute Albrecht
- Southwest Florida Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, 2685 SR 29 North, Immokalee, FL 34142, USA; US Horticultural Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 2001 South Rock Rd., Fort Pierce, FL 34945, USA.
| | - Oliver Fiehn
- UC Davis Genome Center - Metabolomics, University of California, 451 Health Drive, Davis, CA 95616, USA; King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia
| | - Kim D Bowman
- US Horticultural Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 2001 South Rock Rd., Fort Pierce, FL 34945, USA
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Domingo-Almenara X, Brezmes J, Vinaixa M, Samino S, Ramirez N, Ramon-Krauel M, Lerin C, Díaz M, Ibáñez L, Correig X, Perera-Lluna A, Yanes O. eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC/MS-Based Metabolomics. Anal Chem 2016; 88:9821-9829. [PMID: 27584001 DOI: 10.1021/acs.analchem.6b02927] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Gas chromatography coupled to mass spectrometry (GC/MS) has been a long-standing approach used for identifying small molecules due to the highly reproducible ionization process of electron impact ionization (EI). However, the use of GC-EI MS in untargeted metabolomics produces large and complex data sets characterized by coeluting compounds and extensive fragmentation of molecular ions caused by the hard electron ionization. In order to identify and extract quantitative information on metabolites across multiple biological samples, integrated computational workflows for data processing are needed. Here we introduce eRah, a free computational tool written in the open language R composed of five core functions: (i) noise filtering and baseline removal of GC/MS chromatograms, (ii) an innovative compound deconvolution process using multivariate analysis techniques based on compound match by local covariance (CMLC) and orthogonal signal deconvolution (OSD), (iii) alignment of mass spectra across samples, (iv) missing compound recovery, and (v) identification of metabolites by spectral library matching using publicly available mass spectra. eRah outputs a table with compound names, matching scores and the integrated area of compounds for each sample. The automated capabilities of eRah are demonstrated by the analysis of GC-time-of-flight (TOF) MS data from plasma samples of adolescents with hyperinsulinaemic androgen excess and healthy controls. The quantitative results of eRah are compared to centWave, the peak-picking algorithm implemented in the widely used XCMS package, MetAlign, and ChromaTOF software. Significantly dysregulated metabolites are further validated using pure standards and targeted analysis by GC-triple quadrupole (QqQ) MS, LC-QqQ, and NMR. eRah is freely available at http://CRAN.R-project.org/package=erah .
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Affiliation(s)
- Xavier Domingo-Almenara
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili , 43003 Tarragona, Catalonia, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain
| | - Jesus Brezmes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili , 43003 Tarragona, Catalonia, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain
| | - Maria Vinaixa
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili , 43003 Tarragona, Catalonia, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain
| | - Sara Samino
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili , 43003 Tarragona, Catalonia, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain
| | - Noelia Ramirez
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili , 43003 Tarragona, Catalonia, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain
| | - Marta Ramon-Krauel
- Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, University of Barcelona , 08950 Barcelona, Catalonia, Spain
| | - Carles Lerin
- Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, University of Barcelona , 08950 Barcelona, Catalonia, Spain
| | - Marta Díaz
- Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain.,Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, University of Barcelona , 08950 Barcelona, Catalonia, Spain
| | - Lourdes Ibáñez
- Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain.,Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, University of Barcelona , 08950 Barcelona, Catalonia, Spain
| | - Xavier Correig
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili , 43003 Tarragona, Catalonia, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain
| | - Alexandre Perera-Lluna
- B2SLab, Center for Biomedical Engineering Research (CREB), CIBERBBN, Department of ESAII, Universitat Politècnica de Catalunya , 08028 Barcelona, Catalonia, Spain
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili , 43003 Tarragona, Catalonia, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , 28029 Madrid, Spain
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Lee JE, Lee YH, Kim SY, Kim YG, Moon JY, Jeong KH, Lee TW, Ihm CG, Kim S, Kim KH, Kim DK, Kim YS, Kim CD, Park CW, Lee DY, Lee SH. Systematic biomarker discovery and coordinative validation for different primary nephrotic syndromes using gas chromatography-mass spectrometry. J Chromatogr A 2016; 1453:105-15. [PMID: 27247212 DOI: 10.1016/j.chroma.2016.05.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/04/2016] [Accepted: 05/15/2016] [Indexed: 11/24/2022]
Abstract
The goal of this study is to identify systematic biomarker panel for primary nephrotic syndromes from urine samples by applying a non-target metabolite profiling, and to validate their utility in independent sampling and analysis by multiplex statistical approaches. Nephrotic syndrome (NS) is a nonspecific kidney disorder, which is mostly represented by minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and membranous glomerulonephritis (MGN). Since urine metabolites may mirror disease-specific functional perturbations in kidney injury, we examined urine samples for distinctive metabolic changes to identify biomarkers for clinical applications. We developed unbiased multi-component covarianced models from a discovery set with 48 samples (12 healthy controls, 12 MCD, 12 FSGS, and 12 MGN). To extensively validate their diagnostic potential, new batch from 54 patients with primary NS were independently examined a year after. In the independent validation set, the model including citric acid, pyruvic acid, fructose, ethanolamine, and cysteine effectively discriminated each NS using receiver operating characteristic (ROC) analysis except MCD-MGN comparison; nonetheless an additional metabolite multi-composite greatly improved the discrimination power between MCD and MGN. Finally, we proposed the re-constructed metabolic network distinctively dysregulated by the different NSs that may deepen comprehensive understanding of the disease mechanistic, and help the enhanced identification of NS and therapeutic plans for future.
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Affiliation(s)
- Jung-Eun Lee
- The Dept. of Bio and Fermentation Convergence Technology, BK21 PLUS project, Kookmin University, Seoul, Republic of Korea; Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Yu Ho Lee
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Se-Yun Kim
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Yang Gyun Kim
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Ju-Young Moon
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Kyung-Hwan Jeong
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Tae Won Lee
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Chun-Gyoo Ihm
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Sooah Kim
- The Dept. of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Kyoung Heon Kim
- The Dept. of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Dong Ki Kim
- Division of Nephrology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yon Su Kim
- Division of Nephrology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chan-Duck Kim
- Division of Nephrology, Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Cheol Whee Park
- Division of Nephrology, Department of Internal Medicine, College of Medicine, The St. Mary's Hospital of Catholic University of Korea, Seoul, Republic of Korea
| | - Do Yup Lee
- The Dept. of Bio and Fermentation Convergence Technology, BK21 PLUS project, Kookmin University, Seoul, Republic of Korea.
| | - Sang-Ho Lee
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea.
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50
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Han S, Micallef SA. Environmental Metabolomics of the Tomato Plant Surface Provides Insights on Salmonella enterica Colonization. Appl Environ Microbiol 2016; 82:3131-3142. [PMID: 26994076 PMCID: PMC4959065 DOI: 10.1128/aem.00435-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/14/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Foodborne illness-causing enteric bacteria are able to colonize plant surfaces without causing infection. We lack an understanding of how epiphytic persistence of enteric bacteria occurs on plants, possibly as an adaptive transit strategy to maximize chances of reentering herbivorous hosts. We used tomato (Solanum lycopersicum) cultivars that have exhibited differential susceptibilities to Salmonella enterica colonization to investigate the influence of plant surface compounds and exudates on enteric bacterial populations. Tomato fruit, shoot, and root exudates collected at different developmental stages supported growth of S. enterica to various degrees in a cultivar- and plant organ-dependent manner. S. enterica growth in fruit exudates of various cultivars correlated with epiphytic growth data (R(2) = 0.504; P = 0.006), providing evidence that plant surface compounds drive bacterial colonization success. Chemical profiling of tomato surface compounds with gas chromatography-time of flight mass spectrometry (GC-TOF-MS) provided valuable information about the metabolic environment on fruit, shoot, and root surfaces. Hierarchical cluster analysis of the data revealed quantitative differences in phytocompounds among cultivars and changes over a developmental course and by plant organ (P < 0.002). Sugars, sugar alcohols, and organic acids were associated with increased S. enterica growth, while fatty acids, including palmitic and oleic acids, were negatively correlated. We demonstrate that the plant surface metabolite landscape has a significant impact on S. enterica growth and colonization efficiency. This environmental metabolomics approach provides an avenue to understand interactions between human pathogens and plants that could lead to strategies to identify or breed crop cultivars for microbiologically safer produce. IMPORTANCE In recent years, fresh produce has emerged as a leading food vehicle for enteric pathogens. Salmonella-contaminated tomatoes represent a recurrent human pathogen-plant commodity pair. We demonstrate that Salmonella can utilize tomato surface compounds and exudates for growth. Surface metabolite profiling revealed that the types and amounts of compounds released to the plant surface differ by cultivar, plant developmental stage, and plant organ. Differences in exudate profiles explain some of the variability in Salmonella colonization susceptibility seen among tomato cultivars. Certain medium- and long-chain fatty acids were associated with restricted Salmonella growth, while sugars, sugar alcohols, and organic acids correlated with larger Salmonella populations. These findings uncover the possibility of selecting crop varieties based on characteristics that impair foodborne pathogen growth for enhanced safety of fresh produce.
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Affiliation(s)
- Sanghyun Han
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
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