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Domingo-Ortí I, Ferrer-Torres P, Armiñán A, Vicent MJ, Pineda-Lucena A, Palomino-Schätzlein M. NMR-Based Mitochondria Metabolomic Profiling: A New Approach To Reveal Cancer-Associated Alterations. Anal Chem 2023; 95:16539-16548. [PMID: 37906730 DOI: 10.1021/acs.analchem.3c02432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Studying metabolism may assist in understanding the relationship between normal and dysfunctional mitochondrial activity and various diseases, such as neurodegenerative, cardiovascular, autoimmune, psychiatric, and cancer. Nuclear magnetic resonance-based metabolomics represents a powerful method to characterize the chemical content of complex samples and has been successfully applied to studying a range of conditions. However, an optimized methodology is lacking for analyzing isolated organelles, such as mitochondria. In this study, we report the development of a protocol to metabolically profile mitochondria from healthy, tumoral, and metastatic tissues. Encouragingly, this approach provided quantitative information about up to 45 metabolites in one comprehensive and robust analysis. Our results revealed significant differences between whole-cell and mitochondrial metabolites, which supports a more refined approach to metabolic analysis. We applied our optimized methodology to investigate aggressive and metastatic breast cancer in mouse tissues, discovering that lung mitochondria exhibit an altered metabolic fingerprint. Specific amino acids, organic acids, and lipids showed significant increases in levels when compared with mitochondria from healthy tissues. Our optimized methodology could promote a better understanding of the molecular mechanisms underlying breast cancer aggressiveness and mitochondrial-related diseases and support the optimization of new advanced therapies.
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Affiliation(s)
- Inés Domingo-Ortí
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Laboratory and CIBERONC, Valencia 46012, Spain
- NMR Facility, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain
| | | | - Ana Armiñán
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Laboratory and CIBERONC, Valencia 46012, Spain
| | - María J Vicent
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Laboratory and CIBERONC, Valencia 46012, Spain
| | - Antonio Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain
- Molecular Therapeutics Program, CIMA Universidad de Navarra, Pamplona 31008, Spain
| | - Martina Palomino-Schätzlein
- NMR Facility, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
- ProtoQSAR, CEEI, Parque Tecnológico Valencia, Paterna 46980, Spain
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2
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Yang W, Zhang X, Sun M, Jiao Y, Li X, Liu L, Wang Z. The Peptide Fractions of Cheddar Cheese Made with Lactobacillus helveticus 1.0612 Play Protective Effects in H 2O 2-Induced Oxidative-Damaged Caco-2 Cells Models. Foods 2023; 12:2790. [PMID: 37509882 PMCID: PMC10379991 DOI: 10.3390/foods12142790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
In this study, water-soluble peptide (WSP) fractions of cheddar cheese made with Lactobacillus helveticus 1.0612 were purified into WSP-Ⅰ (<3 kDa), WSP-Ⅱ (3-10 kDa), and WSP-Ⅲ (>10 kDa). The protective effects of WSP, WSP-Ⅰ, WSP-Ⅱ, and WSP-Ⅲ fractions against oxidative stress in Caco-2 cells were assayed, and the cytoprotective mechanism of WSP-Ⅰ on cells oxidative damage was elucidated via metabolomics. The results showed that all four peptide fractions were able to attenuate the decrease in cell viability caused by oxidative stress and also could reduce the production of reactive oxygen species and malondialdehyde caused by oxidative stress, and increased cellular catalase and superoxide dismutase activities, thereby enhancing cellular antioxidant capacity. The WSP-Ⅰ fraction with the highest protective effect was used for metabolomics analysis, and 15 significantly different metabolites were screened. Functional pathway analysis revealed that the protective effect of the WSP-I fraction was related with nine metabolic pathways and weakened the metabolic disorders caused by H2O2 via regulating energy metabolism and amino acid metabolism. All in all, peptide fractions of cheddar cheese showed a cytoprotective effect through improved cellular metabolism.
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Affiliation(s)
- Wanshuang Yang
- College of Food Science, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
| | - Xiuxiu Zhang
- College of Food Science, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
| | - Meng Sun
- College of Food Science, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
| | - Yang Jiao
- College of Food Science, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
| | - Xiaodong Li
- College of Food Science, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
| | - Lu Liu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
| | - Zhong Wang
- College of Food Science, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, No. 600 Changjiang St., Xiangfang Dist., Harbin 150030, China
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Hwang H, Liu R, Eldridge R, Hu X, Forghani P, Jones DP, Xu C. Chronic ethanol exposure induces mitochondrial dysfunction and alters gene expression and metabolism in human cardiac spheroids. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2023; 47:643-658. [PMID: 36799338 PMCID: PMC10149610 DOI: 10.1111/acer.15026] [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: 12/07/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
BACKGROUND Chronic alcohol consumption in adults can induce various cardiac toxicities such as arrhythmias, cardiomyopathy, and heart failure. Prenatal alcohol exposure can increase the risk of developing congenital heart defects among offspring. Understanding the molecular mechanisms underlying long-term alcohol exposure-induced cardiotoxicity can help guide the development of therapeutic strategies. METHODS Cardiomyocytes derived from human-induced pluripotent stem cells (hiPSC-CMs) were engineered into cardiac spheroids and treated with clinically relevant concentrations of ethanol (17 and 50 mM) for 5 weeks. The cells were then analyzed for changes in mitochondrial features, transcriptomic and metabolomic profiles, and integrated omics outcomes. RESULTS Following chronic ethanol treatment of hiPSC-CMs, a decrease in mitochondrial membrane potential and respiration and changes in expression of mitochondrial function-related genes were observed. RNA-sequencing analysis revealed changes in various metabolic processes, heart development, response to hypoxia, and extracellular matrix-related activities. Metabolomic analysis revealed dysregulation of energy metabolism and increased metabolites associated with the upregulation of inflammation. Integrated omics analysis further identified functional subclusters and revealed potentially affected pathways associated with cardiac toxicities. CONCLUSION Chronic ethanol treatment of hiPSC-CMs resulted in overall decreased mitochondrial function, increased glycolysis, disrupted fatty acid oxidation, and impaired cardiac structural development.
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Affiliation(s)
- Hyun Hwang
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Rui Liu
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Ronald Eldridge
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA 30322, USA
| | - Xin Hu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Parvin Forghani
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Chunhui Xu
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
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Qin S, Zhang Y, Tian Y, Xu F, Zhang P. Subcellular metabolomics: Isolation, measurement, and applications. J Pharm Biomed Anal 2021; 210:114557. [PMID: 34979492 DOI: 10.1016/j.jpba.2021.114557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/26/2022]
Abstract
Metabolomics, a technique that profiles global small molecules in biological samples, has been a pivotal tool for disease diagnosis and mechanism research. The sample type in metabolomics covers a wide range, including a variety of body fluids, tissues, and cells. However, little attention was paid to the smaller, relatively independent partition systems in cells, namely the organelles. The organelles are specific compartments/places where diverse metabolic activities are happening in an orderly manner. Metabolic disorders of organelles were found to occur in various pathological conditions such as inherited metabolic diseases, diabetes, cancer, and neurodegenerative diseases. However, at the cellular level, the metabolic outcomes of organelles and cytoplasm are superimposed interactively, making it difficult to describe the changes in subcellular compartments. Therefore, characterizing the metabolic pool in the compartmentalized system is of great significance for understanding the role of organelles in physiological functions and diseases. So far, there are very few research articles or reviews related to subcellular metabolomics. In this review, subcellular fractionation and metabolite analysis methods, as well as the application of subcellular metabolomics in the physiological and pathological studies are systematically reviewed, as a practical reference to promote the continued advancement in subcellular metabolomics.
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Affiliation(s)
- Siyuan Qin
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yuxin Zhang
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, PR China
| | - Yuan Tian
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Pei Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
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Liu KH, Owens JA, Saeedi B, Cohen CE, Bellissimo MP, Naudin C, Darby T, Druzak S, Maner-Smith K, Orr M, Hu X, Fernandes J, Camacho MC, Hunter-Chang S, VanInsberghe D, Ma C, Ganesh T, Yeligar SM, Uppal K, Go YM, Alvarez JA, Vos MB, Ziegler TR, Woodworth MH, Kraft CS, Jones RM, Ortlund E, Neish AS, Jones DP. Microbial metabolite delta-valerobetaine is a diet-dependent obesogen. Nat Metab 2021; 3:1694-1705. [PMID: 34931082 PMCID: PMC8711632 DOI: 10.1038/s42255-021-00502-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/04/2021] [Indexed: 12/17/2022]
Abstract
Obesity and obesity-related metabolic disorders are linked to the intestinal microbiome. However, the causality of changes in the microbiome-host interaction affecting energy metabolism remains controversial. Here, we show the microbiome-derived metabolite δ-valerobetaine (VB) is a diet-dependent obesogen that is increased with phenotypic obesity and is correlated with visceral adipose tissue mass in humans. VB is absent in germ-free mice and their mitochondria but present in ex-germ-free conventionalized mice and their mitochondria. Mechanistic studies in vivo and in vitro show VB is produced by diverse bacterial species and inhibits mitochondrial fatty acid oxidation through decreasing cellular carnitine and mitochondrial long-chain acyl-coenzyme As. VB administration to germ-free and conventional mice increases visceral fat mass and exacerbates hepatic steatosis with a western diet but not control diet. Thus, VB provides a molecular target to understand and potentially manage microbiome-host symbiosis or dysbiosis in diet-dependent obesity.
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Affiliation(s)
- Ken H Liu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua A Owens
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Bejan Saeedi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Catherine E Cohen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Moriah P Bellissimo
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Crystal Naudin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Trevor Darby
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Samuel Druzak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Kristal Maner-Smith
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael Orr
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jolyn Fernandes
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Mary Catherine Camacho
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Hunter-Chang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - David VanInsberghe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Chunyu Ma
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Thota Ganesh
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Samantha M Yeligar
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Atlanta Veterans Affairs Health Care System, Decatur, GA, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jessica A Alvarez
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Miriam B Vos
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas R Ziegler
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael H Woodworth
- Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rheinallt M Jones
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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Yu EA, He S, Jones DP, Sun YV, Ramirez-Zea M, Stein AD. Metabolomic Profiling Demonstrates Postprandial Changes in Fatty Acids and Glycerophospholipids Are Associated with Fasting Inflammation in Guatemalan Adults. J Nutr 2021; 151:2564-2573. [PMID: 34113999 PMCID: PMC8417933 DOI: 10.1093/jn/nxab183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/25/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Metabolic flexibility is the responsiveness to heterogeneous physiological conditions, such as food ingestion. A key unresolved question is how inflammation affects metabolic flexibility. OBJECTIVES Our study objective was to compare metabolic flexibility, specifically the metabolomic response to a standardized meal, by fasting inflammation status. METHODS Participants in Guatemala (n = 302, median age 44 y, 43.7% men) received a standardized, mixed-macronutrient liquid meal. Plasma samples (fasting, 2 h postmeal) were assayed by dual-column LC [reverse phase (C18) and hydrophilic interaction LC (HILIC)] with ultra-high-resolution MS, for concentrations of 6 inflammation biomarkers: high-sensitivity C-reactive protein (hsCRP), leptin, resistin, IL-10, adiponectin, and soluble TNF receptor II (TNFsR). We summed the individual inflammation biomarker z-scores, after reverse-coding of anti-inflammation biomarkers. We identified features with peak areas that differed between fasting and postmeal (false discovery rate-adjusted q <0.05) and compared median log2 postprandial/fasting peak area ratios by inflammation indicators. RESULTS We found 1397 C18 and 974 HILIC features with significant postprandial/fasting feature ratios (q <0.05). Overall inflammation z-score was directly associated with the postprandial/fasting feature ratios of arachidic acid, and inversely associated with the feature ratio of lysophosphatidic acid (LPA), adjusting for age and sex (all P < 0.05). The postprandial/fasting ratio of arachidic acid was negatively correlated with resistin, IL-10, adiponectin, and TNFsR concentrations (all P < 0.05). Feature ratios of several fatty acids-myristic acid [m/z 227.2018, retention time (RT) 229], heptadecanoic acid (m/z 269.2491, RT 276), linoleic acid (m/z 280.2358, RT 236)-were negatively correlated with fasting plasma concentrations of leptin (nanograms per milliliter) and adiponectin (micrograms per milliliter), respectively (all P < 0.05). The postprandial/fasting ratio of LPA was positively correlated with IL-10 and adiponectin (both P < 0.05); and the ratio of phosphatidylinositol was positively correlated with hsCRP (P < 0.05). CONCLUSIONS Postprandial responses of fatty acids and glycerophospholipids are associated with fasting inflammation status in adults in Guatemala.
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Affiliation(s)
- Elaine A Yu
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Siran He
- Nutrition and Health Sciences Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Manuel Ramirez-Zea
- INCAP Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala City, Guatemala
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Li H, Uittenbogaard M, Hao L, Chiaramello A. Clinical Insights into Mitochondrial Neurodevelopmental and Neurodegenerative Disorders: Their Biosignatures from Mass Spectrometry-Based Metabolomics. Metabolites 2021; 11:233. [PMID: 33920115 PMCID: PMC8070181 DOI: 10.3390/metabo11040233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are dynamic multitask organelles that function as hubs for many metabolic pathways. They produce most ATP via the oxidative phosphorylation pathway, a critical pathway that the brain relies on its energy need associated with its numerous functions, such as synaptic homeostasis and plasticity. Therefore, mitochondrial dysfunction is a prevalent pathological hallmark of many neurodevelopmental and neurodegenerative disorders resulting in altered neurometabolic coupling. With the advent of mass spectrometry (MS) technology, MS-based metabolomics provides an emerging mechanistic understanding of their global and dynamic metabolic signatures. In this review, we discuss the pathogenetic causes of mitochondrial metabolic disorders and the recent MS-based metabolomic advances on their metabolomic remodeling. We conclude by exploring the MS-based metabolomic functional insights into their biosignatures to improve diagnostic platforms, stratify patients, and design novel targeted therapeutic strategies.
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Affiliation(s)
- Haorong Li
- Department of Chemistry, George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, DC 20052, USA;
| | - Martine Uittenbogaard
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, 2300 I Street N.W. Ross Hall 111, Washington, DC 20037, USA;
| | - Ling Hao
- Department of Chemistry, George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, DC 20052, USA;
| | - Anne Chiaramello
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, 2300 I Street N.W. Ross Hall 111, Washington, DC 20037, USA;
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Yu EA, Yu T, Jones DP, Ramirez-Zea M, Stein AD. Metabolomic Profiling After a Meal Shows Greater Changes and Lower Metabolic Flexibility in Cardiometabolic Diseases. J Endocr Soc 2020; 4:bvaa127. [PMID: 33134764 PMCID: PMC7584117 DOI: 10.1210/jendso/bvaa127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
Context Metabolic flexibility is the physiologic acclimatization to differing energy availability and requirement states. Effectively maintaining metabolic flexibility remains challenging, particularly since metabolic dysregulations in meal consumption during cardiometabolic disease (CMD) pathophysiology are incompletely understood. Objective We compared metabolic flexibility following consumption of a standardized meal challenge among adults with or without CMDs. Design, Setting, and Participants Study participants (n = 349; age 37-54 years, 55% female) received a standardized meal challenge (520 kcal, 67.4 g carbohydrates, 24.3 g fat, 8.0 g protein; 259 mL). Blood samples were collected at baseline and 2 hours postchallenge. Plasma samples were assayed by high-resolution, nontargeted metabolomics with dual-column liquid chromatography and ultrahigh-resolution mass spectrometry. Metabolome-wide associations between features and meal challenge timepoint were assessed in multivariable linear regression models. Results Sixty-five percent of participants had ≥1 of 4 CMDs: 33% were obese, 6% had diabetes, 39% had hypertension, and 50% had metabolic syndrome. Log2-normalized ratios of feature peak areas (postprandial:fasting) clustered separately among participants with versus without any CMDs. Among participants with CMDs, the meal challenge altered 1756 feature peak areas (1063 reversed-phase [C18], 693 hydrophilic interaction liquid chromatography [HILIC]; all q < 0.05). In individuals without CMDs, the meal challenge changed 1383 feature peak areas (875 C18; 508 HILIC; all q < 0.05). There were 108 features (60 C18; 48 HILIC) that differed by the meal challenge and CMD status, including dipeptides, carnitines, glycerophospholipids, and a bile acid metabolite (all P < 0.05). Conclusions Among adults with CMDs, more metabolomic features differed after a meal challenge, which reflected lower metabolic flexibility relative to individuals without CMDs.
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Affiliation(s)
- Elaine A Yu
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Tianwei Yu
- School of Data Science, Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong Province, China
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, Emory University, Atlanta, Georgia
| | - Manuel Ramirez-Zea
- Institute of Nutrition of Central America and Panama Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala City, Guatemala
| | - Aryeh D Stein
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
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9
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Yu EA, Yu T, Jones DP, Martorell R, Ramirez-Zea M, Stein AD. Macronutrient, Energy, and Bile Acid Metabolism Pathways Altered Following a Physiological Meal Challenge, Relative to Fasting, among Guatemalan Adults. J Nutr 2020; 150:2031-2040. [PMID: 32597983 PMCID: PMC7398776 DOI: 10.1093/jn/nxaa169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/06/2020] [Accepted: 05/19/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The healthy human metabolome, including its physiological responses after meal consumption, remains incompletely understood. One major research gap is the limited literature assessing how human metabolomic profiles differ between fasting and postprandial states after physiological challenges. OBJECTIVES Our study objective was to evaluate alterations in high-resolution metabolomic profiles following a standardized meal challenge, relative to fasting, in Guatemalan adults. METHODS We studied 123 Guatemalan adults without obesity, hypertension, diabetes, metabolic syndrome, or comorbidities. Every participant received a standardized meal challenge (520 kcal, 67.4 g carbohydrates, 24.3 g fat, 8.0 g protein) and provided blood samples while fasting and at 2 h postprandial. Plasma samples were assayed by high-resolution metabolomics with dual-column LC [C18 (negative electrospray ionization), hydrophilic interaction LC (HILIC, positive electrospray ionization)] coupled to ultra-high-resolution MS. Associations between metabolomic features and the meal challenge timepoint were assessed in feature-by-feature multivariable linear mixed regression models. Two algorithms (mummichog, gene set enrichment analysis) were used for pathway analysis, and P values were combined by the Fisher method. RESULTS Among participants (62.6% male, median age 43.0 y), 1130 features (C18: 777; HILIC: 353) differed between fasting and postprandial states (all false discovery rate-adjusted q < 0.05). Based on differing C18 features, top pathways included: tricarboxylic acid cycle (TCA), primary bile acid biosynthesis, and linoleic acid metabolism (all Pcombined < 0.05). Mass spectral features included: taurine and cholic acid in primary bile acid biosynthesis; and fumaric acid, malic acid, and citric acid in the TCA. HILIC features that differed in the meal challenge reflected linoleic acid metabolism (Pcombined < 0.05). CONCLUSIONS Energy, macronutrient, and bile acid metabolism pathways were responsive to a standardized meal challenge in adults without cardiometabolic diseases. Our findings reflect metabolic flexibility in disease-free individuals.
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Affiliation(s)
- Elaine A Yu
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Reynaldo Martorell
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Manuel Ramirez-Zea
- Institute of Nutrition of Central America and Panama Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala City, Guatemala
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Volkova S, Matos MRA, Mattanovich M, Marín de Mas I. Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis. Metabolites 2020; 10:E303. [PMID: 32722118 PMCID: PMC7465778 DOI: 10.3390/metabo10080303] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 01/05/2023] Open
Abstract
Metabolic networks are regulated to ensure the dynamic adaptation of biochemical reaction fluxes to maintain cell homeostasis and optimal metabolic fitness in response to endogenous and exogenous perturbations. To this end, metabolism is tightly controlled by dynamic and intricate regulatory mechanisms involving allostery, enzyme abundance and post-translational modifications. The study of the molecular entities involved in these complex mechanisms has been boosted by the advent of high-throughput technologies. The so-called omics enable the quantification of the different molecular entities at different system layers, connecting the genotype with the phenotype. Therefore, the study of the overall behavior of a metabolic network and the omics data integration and analysis must be approached from a holistic perspective. Due to the close relationship between metabolism and cellular phenotype, metabolic modelling has emerged as a valuable tool to decipher the underlying mechanisms governing cell phenotype. Constraint-based modelling and kinetic modelling are among the most widely used methods to study cell metabolism at different scales, ranging from cells to tissues and organisms. These approaches enable integrating metabolomic data, among others, to enhance model predictive capabilities. In this review, we describe the current state of the art in metabolic modelling and discuss future perspectives and current challenges in the field.
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Affiliation(s)
| | | | | | - Igor Marín de Mas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; (S.V.); (M.R.A.M.); (M.M.)
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11
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van der Walt G, Louw R. Novel mitochondrial and cytosolic purification pipeline for compartment-specific metabolomics in mammalian disease model tissues. Metabolomics 2020; 16:78. [PMID: 32577914 DOI: 10.1007/s11306-020-01697-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/13/2020] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Mitochondria represent an important milieu for studying the pathogenesis of several major diseases. The need for organelle-level metabolic resolution exists, as mitochondrial/cytosolic metabolites are often diluted beyond detection limits in complex samples. Compartment-specific studies are still hindered by the lack of efficient, cost-effective fractioning methods-applicable to laboratories of all financial/analytical standing. OBJECTIVES We established a novel mitochondrial/cytosolic purification pipeline for complimentary GC-TOF-MS and 1H-NMR metabolomics using robust, commercially available fractionation strategies. METHODS Magnetic based mitochondria isolation kits (MACS) were adapted for this purpose, accompanied by cytosolic filtering. Yield was assessed through the percentage recovery of citrate synthase (CS; a mitochondrial marker), purity by immunoblotting against compartment-specific proteins and integrity interrogated through the respiratory coupling ratio (RCR). The effects of the kit-based buffers on MS/NMR analyses of pure metabolite standards were evaluated. Finally, biological applicability to mammalian disease models was shown using Ndufs4 mouse brain tissue. RESULTS With minor modifications, MACS produced around 60% more mitochondria compared to a differential centrifugation method. Less than 15% of lysosomal LAMP-2 protein was found in the MACS isolates, confirming relative purity-while RCR's above 6 indicate sufficient mitochondrial integrity. The filtering approach effectively depleted mitochondria from the cytosolic fraction, as indicated by negligible Hsp60 and CS levels. Our GC-MS pilot yielded 60-70 features per fraction, while NMR analyses could quantify 6-10 of the most abundant compounds in each fraction. CONCLUSION This study provides a simple and flexible solution for mitochondrial and cytosolic metabolomics in animal model tissues, towards large-scale application of such methodologies in disease research.
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Affiliation(s)
- Gunter van der Walt
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Potchefstroom, South Africa
| | - Roan Louw
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Potchefstroom, South Africa.
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12
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Saeedi BJ, Liu KH, Owens JA, Hunter-Chang S, Camacho MC, Eboka RU, Chandrasekharan B, Baker NF, Darby TM, Robinson BS, Jones RM, Jones DP, Neish AS. Gut-Resident Lactobacilli Activate Hepatic Nrf2 and Protect Against Oxidative Liver Injury. Cell Metab 2020; 31:956-968.e5. [PMID: 32213347 PMCID: PMC7329068 DOI: 10.1016/j.cmet.2020.03.006] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/09/2020] [Accepted: 03/03/2020] [Indexed: 02/07/2023]
Abstract
Many studies have suggested a role for gut-resident microbes (the "gut microbiome") in modulating host health; however, the mechanisms by which they impact systemic physiology remain largely unknown. In this study, metabolomic and transcriptional profiling of germ-free and conventionalized mouse liver revealed an upregulation of the Nrf2 antioxidant and xenobiotic response in microbiome-replete animals. Using a Drosophila-based screening assay, we identified members of the genus Lactobacillus capable of stimulating Nrf2. Indeed, the human commensal Lactobacillus rhamnosus GG (LGG) potently activated Nrf2 in the Drosophila liver analog and the murine liver. This activation was sufficient to protect against two models of oxidative liver injury, acetaminophen overdose and acute ethanol toxicity. Characterization of the portal circulation of LGG-treated mice by tandem mass spectrometry identified a small molecule activator of Nrf2, 5-methoxyindoleacetic acid, produced by LGG. Taken together, these data demonstrate a mechanism by which intestinal microbes modulate hepatic susceptibility to oxidative injury.
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Affiliation(s)
- Bejan J Saeedi
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ken H Liu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joshua A Owens
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sarah Hunter-Chang
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary C Camacho
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Richard U Eboka
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bindu Chandrasekharan
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nusaiba F Baker
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Trevor M Darby
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Brian S Robinson
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rheinallt M Jones
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S Neish
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA.
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13
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Hu X, Go YM, Jones DP. Omics Integration for Mitochondria Systems Biology. Antioxid Redox Signal 2020; 32:853-872. [PMID: 31891667 PMCID: PMC7074923 DOI: 10.1089/ars.2019.8006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
Significance: Elucidation of the central importance of mitophagy in homeostasis of cells and organisms emphasizes that mitochondrial functions extend far beyond short-term needs for energy production. In mitochondria systems biology, the mitochondrial genome, proteome, and metabolome operate as a functional network in coordination of cell activities. Organization occurs through subnetworks that are interconnected by membrane potential, transport activities, allosteric and cooperative interactions, redox signaling mechanisms, rheostatic control by post-translational modifications, and metal ion homeostasis. These subnetworks enable use of varied energy precursors, defense against environmental stressors, and macromolecular rewiring to titrate energy production, biosynthesis, and detoxification according to cell-specific needs. Rewiring mechanisms, termed mitochondrial reprogramming, enhance fitness to respond to metabolic resources and challenges from the environment. Maladaptive responses can cause cell death. Maladaptive rewiring can cause disease. In cancer, adaptive rewiring can interfere with effective treatment. Recent Advances: Many recent advances have been facilitated by the development of new omics tools, which create opportunities to use data-driven analysis of omics data to address these complex adaptive and maladaptive mechanisms of mitochondrial reprogramming in human disease. Critical Issues: Application of omics integration to model systems reveals a critical role for metal ion homeostasis broadly impacting mitochondrial reprogramming. Importantly, data show that trans-omics associations are more robust and biologically relevant than single omics associations. Future Directions: Application of omics integration to mitophagy research creates new opportunities to link the complex, interactive functions of mitochondrial form and function in mitochondria systems biology.
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Affiliation(s)
- Xin Hu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
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14
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Dennis KK, Uppal K, Liu KH, Ma C, Liang B, Go YM, Jones DP. Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5527149. [PMID: 31267134 PMCID: PMC6606759 DOI: 10.1093/database/baz083] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 12/28/2022]
Abstract
Phytochelatins (PyCs) are a diverse set of plant compounds that chelate metals, protect against metal toxicity and function in metal homeostasis. PyCs are present in plants consumed as food by humans and could, in principle, impact absorption and utilization of essential and toxic metals such as selenium and cadmium, respectively. PyCs vary in terminal amino acid composition and chain length, exist in multiple oxidation states and reversibly bind multiple metals; consequently, PyCs include a large set of possible structures. Although individual PyC-metal complexes have been studied, no resource exists to characterize the diversity of PyCs and PyC-metal complexes. We used the scientific literature to develop a database of elemental formulas for polymer forms varying in chain length from 2 to 11 glutamyl-cysteine repeats. Using elemental formulas, we calculated monoisotopic masses using the most abundant isotopes of each element and calculated masses for complexes with 13 metals of nutritional and toxicological significance. The resulting phytochelatin database (PyCDB) contains 46 260 unique elemental formulas for PyC and PyC-metal complexes. The database is available online for download as well as for direct mass queries for mass spectrometry using an accurate mass annotation tool for user-selected PyC types, metals and adducts of interest. We performed studies of a commonly consumed food—onion—to validate the database and test utility of the tool. Onion samples were analyzed using ultra-high resolution mass spectrometry-based metabolomics. Mass spectral features were annotated using the PyCDB web tool and the R package, xMSannotator; annotated features were further validated by collision-induced dissociation mass spectrometry. The results establish use and a workflow for PyCDB as a resource for characterization of PyCs and PyC-metal complexes.
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Affiliation(s)
- Kristine K Dennis
- Nutrition and Health Sciences, Laney Graduate School, Emory University, Atlanta, GA, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Ken H Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Chunyu Ma
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Bill Liang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Dean P Jones
- Nutrition and Health Sciences, Laney Graduate School, Emory University, Atlanta, GA, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
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15
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Cheung AC, Walker DI, Juran BD, Miller GW, Lazaridis KN. Studying the Exposome to Understand the Environmental Determinants of Complex Liver Diseases. Hepatology 2020; 71:352-362. [PMID: 31701542 PMCID: PMC7329010 DOI: 10.1002/hep.31028] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Angela C. Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Douglas I. Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Brian D. Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Gary W. Miller
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY
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16
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Smith MR, Chacko BK, Johnson MS, Benavides GA, Uppal K, Go YM, Jones DP, Darley-Usmar VM. A precision medicine approach to defining the impact of doxorubicin on the bioenergetic-metabolite interactome in human platelets. Redox Biol 2020; 28:101311. [PMID: 31546171 PMCID: PMC6812033 DOI: 10.1016/j.redox.2019.101311] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/22/2019] [Accepted: 08/30/2019] [Indexed: 12/26/2022] Open
Abstract
Non-invasive measures of the response of individual patients to cancer therapeutics is an emerging strategy in precision medicine. Platelets offer a potential dynamic marker for metabolism and bioenergetic responses in individual patients since they have active glycolysis and mitochondrial oxidative phosphorylation and can be easily isolated from a small blood sample. We have recently shown how the bioenergetic-metabolite interactome can be defined in platelets isolated from human subjects by measuring metabolites and bioenergetics in the same sample. In the present study, we used a model system to assess test the hypothesis that this interactome is modified by xenobiotics using exposure to the anti-cancer drug doxorubicin (Dox) in individual donors. We found that unsupervised analysis of the metabolome showed clear differentiation between the control and Dox treated group. Dox treatment resulted in a concentration-dependent decrease in bioenergetic parameters with maximal respiration being most sensitive and this was associated with significant changes in over 166 features. A metabolome-wide association study of Dox was also conducted, and Dox was found to have associations with metabolites in the glycolytic and TCA cycle pathways. Lastly, network analysis showed the impact of Dox on the bioenergetic-metabolite interactome and revealed profound changes in the regulation of reserve capacity. Taken together, these data support the conclusion that platelets are a suitable platform to predict and monitor therapeutic efficacy as well as anticipate susceptibility to toxicity in the context of precision medicine.
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Affiliation(s)
- Matthew Ryan Smith
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Balu K Chacko
- Mitochondrial Medicine Laboratory, Center for Free Radical Biology, Department of Pathology, University of Alabama at Birmingham, USA
| | - Michelle S Johnson
- Mitochondrial Medicine Laboratory, Center for Free Radical Biology, Department of Pathology, University of Alabama at Birmingham, USA
| | - Gloria A Benavides
- Mitochondrial Medicine Laboratory, Center for Free Radical Biology, Department of Pathology, University of Alabama at Birmingham, USA
| | - Karan Uppal
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Young-Mi Go
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Victor M Darley-Usmar
- Mitochondrial Medicine Laboratory, Center for Free Radical Biology, Department of Pathology, University of Alabama at Birmingham, USA.
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17
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Fernandes J, Chandler JD, Liu KH, Uppal K, Hao L, Hu X, Go YM, Jones DP. Metabolomic Responses to Manganese Dose in SH-SY5Y Human Neuroblastoma Cells. Toxicol Sci 2019; 169:84-94. [PMID: 30715528 PMCID: PMC6484887 DOI: 10.1093/toxsci/kfz028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Manganese (Mn)-associated neurotoxicity has been well recognized. However, Mn is also an essential nutrient to maintain physiological function. Our previous study of human neuroblastoma SH-SY5Y cells showed that Mn treatment comparable to physiological and toxicological concentrations in human brain resulted in different mitochondrial responses, yet cellular metabolic responses associated with such different outcomes remain uncharacterized. Herein, SH-SY5Y cells were examined for metabolic responses discriminated by physiological and toxicological levels of Mn using high-resolution metabolomics (HRM). Before performing HRM, we examined Mn dose (from 0 to100 μM) and time effects on cell death. Although we did not observe any immediate cell death after 5 h exposure to any of the Mn concentrations assessed (0-100 μM), cell loss was present after a 24-h recovery period in cultures treated with Mn ≥ 50 μM. Exposure to Mn for 5 h resulted in a wide range of changes in cellular metabolism including amino acids (AA), neurotransmitters, energy, and fatty acids metabolism. Adaptive responses at 10 μM showed increases in neuroprotective AA metabolites (creatine, phosphocreatine, phosphoserine). A 5-h exposure to 100 µM Mn, a time before any cell death occurred, resulted in decreases in energy and fatty acid metabolites (hexose-1,6 bisphosphate, acyl carnitines). The results show that adjustments in AA metabolism occur in response to Mn that does not cause cell death while disruption in energy and fatty acid metabolism occur in response to Mn that results in subsequent cell death. The present study establishes utility for metabolomics analyses to discriminate adaptive and toxic molecular responses in a human in vitro cellular model that could be exploited in evaluation of Mn toxicity.
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Affiliation(s)
- Jolyn Fernandes
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Joshua D Chandler
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Ken H Liu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Li Hao
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
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18
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Chacko BK, Smith MR, Johnson MS, Benavides G, Culp ML, Pilli J, Shiva S, Uppal K, Go YM, Jones DP, Darley-Usmar VM. Mitochondria in precision medicine; linking bioenergetics and metabolomics in platelets. Redox Biol 2019; 22:101165. [PMID: 30877854 PMCID: PMC6436140 DOI: 10.1016/j.redox.2019.101165] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/27/2019] [Accepted: 03/08/2019] [Indexed: 12/18/2022] Open
Abstract
Mitochondria possess reserve bioenergetic capacity, supporting protection and resilience in the face of disease. Approaches are limited to understand factors that impact mitochondrial functional reserve in humans. We applied the mitochondrial stress test (MST) to platelets from healthy subjects and found correlations between energetic parameters and mitochondrial function. These parameters were not correlated with mitochondrial complex I-IV activities, however, suggesting that other factors affect mitochondrial bioenergetics and metabolism. Platelets from African American patients with sickle cell disease also differed from controls, further showing that other factors impact mitochondrial bioenergetics and metabolism. To test for correlations of platelet metabolites with energetic parameters, we performed an integrated analysis of metabolomics and MST parameters. Subsets of metabolites, including fatty acids and xenobiotics correlated with mitochondrial parameters. The results establish platelets as a platform to integrate bioenergetics and metabolism for analysis of mitochondrial function in precision medicine.
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Affiliation(s)
- Balu K Chacko
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, UK
| | - Matthew R Smith
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Michelle S Johnson
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, UK
| | - Gloria Benavides
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, UK
| | - Matilda L Culp
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, UK
| | - Jyotsna Pilli
- Department of Pharmacology & Chemical Biology, Vascular Medicine Institute, Center for Metabolism & Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sruti Shiva
- Department of Pharmacology & Chemical Biology, Vascular Medicine Institute, Center for Metabolism & Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karan Uppal
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Young-Mi Go
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, GA, USA
| | - Victor M Darley-Usmar
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, UK.
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19
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Niedzwiecki MM, Walker DI, Vermeulen R, Chadeau-Hyam M, Jones DP, Miller GW. The Exposome: Molecules to Populations. Annu Rev Pharmacol Toxicol 2019; 59:107-127. [PMID: 30095351 DOI: 10.1146/annurev-pharmtox-010818-021315] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Derived from the term exposure, the exposome is an omic-scale characterization of the nongenetic drivers of health and disease. With the genome, it defines the phenome of an individual. The measurement of complex environmental factors that exert pressure on our health has not kept pace with genomics and historically has not provided a similar level of resolution. Emerging technologies make it possible to obtain detailed information on drugs, toxicants, pollutants, nutrients, and physical and psychological stressors on an omic scale. These forces can also be assessed at systems and network levels, providing a framework for advances in pharmacology and toxicology. The exposome paradigm can improve the analysis of drug interactions and detection of adverse effects of drugs and toxicants and provide data on biological responses to exposures. The comprehensive model can provide data at the individual level for precision medicine, group level for clinical trials, and population level for public health.
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Affiliation(s)
- Megan M Niedzwiecki
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; ,
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; ,
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322, USA;
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, Netherlands;
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 Utrecht, Netherlands
- MRC/PHE Centre for Environmental Health, Department of Epidemiology and Public Health, Imperial College London, W2 1PG London, United Kingdom;
| | - Marc Chadeau-Hyam
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, Netherlands;
- MRC/PHE Centre for Environmental Health, Department of Epidemiology and Public Health, Imperial College London, W2 1PG London, United Kingdom;
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322, USA;
| | - Gary W Miller
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
- Current affiliation: Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA;
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20
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Hoffman JM, Ross C, Tran V, Promislow DEL, Tardif S, Jones DP. The metabolome as a biomarker of mortality risk in the common marmoset. Am J Primatol 2018; 81:e22944. [PMID: 30585652 DOI: 10.1002/ajp.22944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022]
Abstract
Recently, the common marmoset has been proposed as a non-human primate model of aging. Their short lifespan coupled with pathologies that are similar to humans make them an ideal model to understand the genetic, metabolic, and environmental factors that influence aging and longevity. However, many of the underlying physiological changes that occur with age in the marmoset are unknown. Here, we attempt to determine if individual metabolites are predictive of future death and to recapitulate past metabolomic results after a change in environment (move across the country) was imposed on a colony of marmosets. We first determined that low levels of tryptophan metabolism metabolites were associated with risk of death in a 2-year follow-up in the animals, suggesting these metabolites may be used as future biomarkers of mortality. We also discovered that betaine metabolism and methionine metabolism are associated with aging regardless of environment for the animals, or of metabolomic assay technique. These two metabolic pathways are therefore of particular interest to examine as future targets for health and lifespan extending interventions. Many of the pathways associated with age in our first study of marmoset metabolomics were not found to have significant age effects in our second study, suggesting more work is needed to understand the reproducibility of large scale metabolomic studies in mammalian models. Overall, we were able to show that while several metabolomics markers show promise in understanding health and lifespan relationships with aging, it is possible that choice of technique for assay and reproducibility in these types of studies are still issues that need to be examined further.
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Affiliation(s)
- Jessica M Hoffman
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Corinna Ross
- Department of Science and Mathematics, Texas A&M University San Antonio, San Antonio, Texas
| | - ViLinh Tran
- Division of Pulmonary Allergy and Critical Care, Department of Medicine, Emory University, Atlanta, Georgia.,Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, Seattle, Washington.,Department of Biology, University of Washington, Seattle, Washington
| | - Suzette Tardif
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Dean P Jones
- Division of Pulmonary Allergy and Critical Care, Department of Medicine, Emory University, Atlanta, Georgia.,Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia
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Fernandes J, Hu X, Ryan Smith M, Go YM, Jones DP. Selenium at the redox interface of the genome, metabolome and exposome. Free Radic Biol Med 2018; 127:215-227. [PMID: 29883789 PMCID: PMC6168380 DOI: 10.1016/j.freeradbiomed.2018.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/19/2018] [Accepted: 06/02/2018] [Indexed: 02/06/2023]
Abstract
Selenium (Se) is a redox-active environmental mineral that is converted to only a small number of metabolites and required for a relatively small number of mammalian enzymes. Despite this, dietary and environmental Se has extensive impact on every layer of omics space. This highlights a need for global network response structures to provide reference for targeted, hypothesis-driven Se research. In this review, we survey the Se research literature from the perspective of the responsive physical and chemical barrier between an organism (functional genome) and its environment (exposome), which we have previously termed the redox interface. Recent advances in metabolomics allow molecular phenotyping of the integrated genome-metabolome-exposome structure. Use of metabolomics with transcriptomics to map functional network responses to supplemental Se in mice revealed complex network responses linked to dyslipidemia and weight gain. Central metabolic hubs in the network structure in liver were not directly linked to transcripts for selenoproteins but were, instead, linked to transcripts for glucose transport and fatty acid β-oxidation. The experimental results confirm the survey of research literature in showing that Se interacts with the functional genome through a complex network response structure. The results imply that systematic application of data-driven integrated omics methods to models with controlled Se exposure could disentangle health benefits and risks from Se exposures and also serve more broadly as an experimental paradigm for exposome research.
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Affiliation(s)
- Jolyn Fernandes
- Department of Medicine, Emory University, Atlanta, GA 30322, United States
| | - Xin Hu
- Department of Medicine, Emory University, Atlanta, GA 30322, United States
| | - M Ryan Smith
- Department of Medicine, Emory University, Atlanta, GA 30322, United States
| | - Young-Mi Go
- Department of Medicine, Emory University, Atlanta, GA 30322, United States.
| | - Dean P Jones
- Department of Medicine, Emory University, Atlanta, GA 30322, United States.
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22
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Fernandes J, Chandler JD, Liu KH, Uppal K, Go YM, Jones DP. Putrescine as indicator of manganese neurotoxicity: Dose-response study in human SH-SY5Y cells. Food Chem Toxicol 2018; 116:272-280. [PMID: 29684492 PMCID: PMC6008158 DOI: 10.1016/j.fct.2018.04.042] [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] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/31/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023]
Abstract
Disrupted polyamine metabolism with elevated putrescine is associated with neuronal dysfunction. Manganese (Mn) is an essential nutrient that causes neurotoxicity in excess, but methods to evaluate biochemical responses to high Mn are limited. No information is available on dose-response effects of Mn on putrescine abundance and related polyamine metabolism. The present research was to test the hypothesis that Mn causes putrescine accumulation over a physiologically adequate to toxic concentration range in a neuronal cell line. We used human SH-SY5Y neuroblastoma cells treated with MnCl2 under conditions that resulted in cell death or no cell death after 48 h. Putrescine and other metabolites were analyzed by liquid chromatography-ultra high-resolution mass spectrometry. Putrescine-related pathway changes were identified with metabolome-wide association study (MWAS). Results show that Mn caused a dose-dependent increase in putrescine over a non-toxic to toxic concentration range. MWAS of putrescine showed positive correlations with the polyamine metabolite N8-acetylspermidine, methionine-related precursors, and arginine-associated urea cycle metabolites, while putrescine was negatively correlated with γ-aminobutyric acid (GABA)-related and succinate-related metabolites (P < 0.001, FDR < 0.01). These data suggest that measurement of putrescine and correlated metabolites may be useful to study effects of Mn intake in the high adequate to UL range.
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Affiliation(s)
- Jolyn Fernandes
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Joshua D Chandler
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Ken H Liu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, 30322, USA.
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, 30322, USA.
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Abstract
Many acute and chronic lung diseases could benefit from improved regeneration therapy. In development and throughout life, genetically encoded exposure memory systems allow environmental exposures, diet, and infectious agents to direct subsequent phenotypic adaptation and responses. The impact of such memory systems on lung regeneration is currently unknown. This article provides a brief overview of advances in redox biology and medicine as a framework for elucidating exposure memory and delineating spatiotemporal responses in lung regeneration. New imaging and omics methods enable precise definition to advance knowledge of development and the cumulative changes in lung biochemistry, structure, and cell populations occurring from prior and ongoing exposures. Importantly, conditioning steps may be needed to reverse exposure memory and enable effective regeneration. Thus, to complement developmental biology and regenerative medicine, research programs are needed to gain systematic knowledge of how lifelong exposures impact lung biology and support transition of lung regeneration from hypothetical to practical medicine.
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Cui F, Zhu P, Ji J, Blaženović I, Gholami M, Zhang Y, Sun X. Gas chromatography-mass spectrometry metabolomic study of lipopolysaccharides toxicity on rat basophilic leukemia cells. Chem Biol Interact 2017; 281:81-88. [PMID: 29275087 DOI: 10.1016/j.cbi.2017.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/19/2017] [Accepted: 12/01/2017] [Indexed: 02/08/2023]
Abstract
Lipopolysaccharide (LPS) can lead to uncontrollable cytokine production, fatal sepsis syndrome and depression/multiple organ failure, as pathophysiologic demonstration. Various toxic effects of LPS have been extensively reported, mainly on the toxicity of LPS in cellular level, macrophages or tumor cells, etc. This work aimed on the impact of LPS on mast cell metabolism, which focused on LPS-induced cellular metabolic profiles. Gas chromatography-mass spectrometry (GC-MS) based metabolomics strategy was implemented for the endo-metabolites detection in rat basophilic leukemia (RBL-2H3) cells, treated with 10 μg/mL LPS for 24 h, along with multiple time-dose tests of cells viability/apoptosis. Significantly changes metabolites were mainly involved the metabolism of glycine, serine, threonine and the biosynthesis of phenylalanine, tyrosine, tryptophan and pentose phosphate pathway. The endo-metabolism results illustrated that LPS treatment led to downregulation of glycine, serine and threonine metabolism besides pentose phosphate pathway in RBL-2H3 cells. This novel insight into LPS cellular metabolism, provides some heuristic guidance for elucidating the underlying mechanism of LPS-mediated disease.
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Affiliation(s)
- Fangchao Cui
- School 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 214122, China
| | - Pei Zhu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China
| | - Jian Ji
- School 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 214122, China
| | | | - Morteza Gholami
- Department of Chemistry, Faculty of Sciences, Golestan University, Gorgan, Iran
| | - Yinzhi Zhang
- School 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 214122, China
| | - Xiulan Sun
- School 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 214122, China.
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25
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Liu X, Xu G. Recent advances in using mass spectrometry for mitochondrial metabolomics and lipidomics - A review. Anal Chim Acta 2017; 1037:3-12. [PMID: 30292306 DOI: 10.1016/j.aca.2017.11.080] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023]
Abstract
Metabolomics and lipidomics generally targets a huge number of intermediate and end products of cellular metabolism in body fluids, tissues, and cells etc. At present, mass spectrometry (MS) based metabolic or lipid profiling of routine biological specimens including the whole cells, tissues, plasma, serum and urine etc., can cover hundreds of metabolites or lipid species in one analysis, which has qualified deep elucidation of global metabolic and lipid networks. Mitochondria are important intracellular organelles and many critical biochemical reactions occur here, they provide building block for new cells, control redox balance, participate in apoptosis and behave as a signalling platform. Evidence suggests high prevalence of mitochondrial dysfunction occurs in a variety of cancers and other diseases, thus there is an urgent demand for investigating and clarifying mitochondrial metabolic and lipid alterations induced by diseases. Nevertheless, mitochondria contribute a small fraction to cellular contents, profiling of whole cell is probably unsuitable for monitoring alterations in mitochondria. Therefore, metabolomics and lipidomics analyses specially for mitochondria are necessary to understand disturbed metabolic and lipid pathways induced by environment and diseases. However, methods for comprehensively profiling metabolites and lipids in mitochondria have been limited at present. This review summarizes the current states and progress of MS-based mitochondrial metabolomics and lipidomics study. Details of mitochondrial isolation procedure, analytical methods and their applications are described. The challenges and opportunities are also given.
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Affiliation(s)
- Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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26
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Dennis KK, Marder E, Balshaw DM, Cui Y, Lynes MA, Patti GJ, Rappaport SM, Shaughnessy DT, Vrijheid M, Barr DB. Biomonitoring in the Era of the Exposome. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:502-510. [PMID: 27385067 PMCID: PMC5381997 DOI: 10.1289/ehp474] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/10/2016] [Accepted: 06/21/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND The term "exposome" was coined in 2005 to underscore the importance of the environment to human health and to bring research efforts in line with those on the human genome. The ability to characterize environmental exposures through biomonitoring is key to exposome research efforts. OBJECTIVES Our objectives were to describe why traditional and nontraditional (exposomic) biomonitoring are both critical in studies aiming to capture the exposome and to make recommendations on how to transition exposure research toward exposomic approaches. We describe the biomonitoring needs of exposome research and approaches and recommendations that will help fill the gaps in the current science. DISCUSSION Traditional and exposomic biomonitoring approaches have key advantages and disadvantages for assessing exposure. Exposomic approaches differ from traditional biomonitoring methods in that they can include all exposures of potential health significance, whether from endogenous or exogenous sources. Issues of sample availability and quality, identification of unknown analytes, capture of nonpersistent chemicals, integration of methods, and statistical assessment of increasingly complex data sets remain challenges that must continue to be addressed. CONCLUSIONS To understand the complexity of exposures faced throughout the lifespan, both traditional and nontraditional biomonitoring methods should be used. Through hybrid approaches and the integration of emerging techniques, biomonitoring strategies can be maximized in research to define the exposome.
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Affiliation(s)
- Kristine K. Dennis
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Elizabeth Marder
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - David M. Balshaw
- Exposure, Response, and Technology Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Yuxia Cui
- Exposure, Response, and Technology Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Michael A. Lynes
- Department of Molecular and Cell Biology, College of Liberal Arts and Sciences, University of Connecticut, Storrs, Connecticut, USA
| | - Gary J. Patti
- Department of Chemistry, and
- Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - Stephen M. Rappaport
- Department of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Daniel T. Shaughnessy
- Exposure, Response, and Technology Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Martine Vrijheid
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Dana Boyd Barr
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Address correspondence to D.B. Barr, Department of Environmental Health, Rollins School of Public Health, 1518 Clifton Rd. NE, Mailstop: 1518-002-2BB. Emory University, Atlanta, GA 30322 USA. Telephone: (404) 727-9605. E-mail:
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27
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Cellular Metabolomics Revealed the Cytoprotection of Amentoflavone, a Natural Compound, in Lipopolysaccharide-Induced Injury of Human Umbilical Vein Endothelial Cells. Int J Mol Sci 2016; 17:ijms17091514. [PMID: 27618027 PMCID: PMC5037791 DOI: 10.3390/ijms17091514] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/01/2016] [Accepted: 09/05/2016] [Indexed: 12/19/2022] Open
Abstract
Amentoflavone is one of the important bioactive flavonoids in the ethylacetate extract of “Cebaiye”, which is a blood cooling and hematostatic herb in traditional Chinese medicine. The previous work in our group has demonstrated that the ethylacetate extract of Cebaiye has a notable antagonistic effect on the injury induced by lipopolysaccharide (LPS) to human umbilical vein endothelial cells (HUVECs). The present investigation was designed to assess the effects and possible mechanism of cytoprotection of amentoflavone via metabolomics. Ultra-performance liquid chromatography/quadrupole time of flight-mass spectrometry (UPLC/QTOF-MS) coupled with multivariate data analysis was used to characterize the variations in the metabolites of HUVECs in response to exposure to LPS and amentoflavone treatment. Seven putative metabolites (glycine, argininosuccinic acid, putrescine, ornithine, spermidine, 5-oxoproline and dihydrouracil) were discovered in cells incubated with LPS and/or amentoflavone. Functional pathway analysis uncovered that the changes of these metabolites related to various significant metabolic pathways (glutathione metabolism, arginine and proline metabolism, β-alanine metabolism and glycine, serine and threonine metabolism), which may explain the potential cytoprotection function of amentoflavone. These findings also demonstrate that cellular metabolomics through UPLC/QTOF-MS is a powerful tool for detecting variations in a range of intracellular compounds upon toxin and/or drug exposure.
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28
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Walker DI, Mallon T, Hopke PK, Uppal K, Go YM, Rohrbeck P, Pennell KD, Jones DP. Deployment-Associated Exposure Surveillance With High-Resolution Metabolomics. J Occup Environ Med 2016; 58:S12-21. [PMID: 27501099 PMCID: PMC4978191 DOI: 10.1097/jom.0000000000000768] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The aim of this study was to assess the suitability of high-resolution metabolomics (HRM) for measure of internal exposure and effect biomarkers from deployment-related environmental hazards. METHODS HRM provides extensive coverage of metabolism and data relevant to a broad spectrum of environmental exposures. This review briefly describes the analytic platform, workflow, and recent applications of HRM as a prototype environmental exposure surveillance system. RESULTS Building upon techniques available for contemporary occupational medicine and exposure sciences, HRM methods are able to integrate external exposures, internal body burden of environmental agents, and relevant biological responses with health outcomes. CONCLUSIONS Systematic analysis of existing Department of Defense Serum Repository samples will provide a high-quality, cross-sectional reference dataset for deployment-associated exposures while at the same time establishing a foundation for precision medicine.
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Affiliation(s)
- Douglas I. Walker
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta GA
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA
| | - Timothy Mallon
- Department of Preventative Medicine & Biometrics, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Philip K. Hopke
- Center for Air Resources Engineering and Science, Clarkson University, Potsdam, NY
| | - Karan Uppal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta GA
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta GA
| | | | - Kurt D. Pennell
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta GA
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29
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High-Resolution Metabolomics for Nutrition and Health Assessment of Armed Forces Personnel. J Occup Environ Med 2016; 58:S80-8. [DOI: 10.1097/jom.0000000000000770] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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30
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Chandler JD, Wongtrakool C, Banton SA, Li S, Orr ML, Barr DB, Neujahr DC, Sutliff RL, Go YM, Jones DP. Low-dose oral cadmium increases airway reactivity and lung neuronal gene expression in mice. Physiol Rep 2016; 4:e12821. [PMID: 27401458 PMCID: PMC4945833 DOI: 10.14814/phy2.12821] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/15/2016] [Indexed: 01/05/2023] Open
Abstract
Inhalation of cadmium (Cd) is associated with lung diseases, but less is known concerning pulmonary effects of Cd found in the diet. Cd has a decades-long half-life in humans and significant bioaccumulation occurs with chronic dietary intake. We exposed mice to low-dose CdCl2 (10 mg/L in drinking water) for 20 weeks, which increased lung Cd to a level similar to that of nonoccupationally exposed adult humans. Cd-treated mice had increased airway hyperresponsiveness to methacholine challenge, and gene expression array showed that Cd altered the abundance of 443 mRNA transcripts in mouse lung. In contrast to higher doses, low-dose Cd did not elicit increased metallothionein transcripts in lung. To identify pathways most affected by Cd, gene set enrichment of transcripts was analyzed. Results showed that major inducible targets of low-dose Cd were neuronal receptors represented by enriched olfactory, glutamatergic, cholinergic, and serotonergic gene sets. Olfactory receptors regulate chemosensory function and airway hypersensitivity, and these gene sets were the most enriched. Targeted metabolomics analysis showed that Cd treatment also increased metabolites in pathways of glutamatergic (glutamate), serotonergic (tryptophan), cholinergic (choline), and catecholaminergic (tyrosine) receptors in the lung tissue. Protein abundance measurements showed that the glutamate receptor GRIN2A was increased in mouse lung tissue. Together, these results show that in mice, oral low-dose Cd increased lung Cd to levels comparable to humans, increased airway hyperresponsiveness and disrupted neuronal pathways regulating bronchial tone. Therefore, dietary Cd may promote or worsen airway hyperresponsiveness in multiple lung diseases including asthma.
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Affiliation(s)
- Joshua D Chandler
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Cherry Wongtrakool
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia Atlanta VA Medical Center, Decatur, Georgia
| | - Sophia A Banton
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Shuzhao Li
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Michael L Orr
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Dana Boyd Barr
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - David C Neujahr
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Roy L Sutliff
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia Atlanta VA Medical Center, Decatur, Georgia
| | - Young-Mi Go
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Dean P Jones
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
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31
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Hoffman JM, Tran V, Wachtman LM, Green CL, Jones DP, Promislow DEL. A longitudinal analysis of the effects of age on the blood plasma metabolome in the common marmoset, Callithrix jacchus. Exp Gerontol 2016; 76:17-24. [PMID: 26805607 DOI: 10.1016/j.exger.2016.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/13/2022]
Abstract
Primates tend to be long-lived for their size with humans being the longest lived of all primates. There are compelling reasons to understand the underlying age-related processes that shape human lifespan. But the very fact of our long lifespan that makes it so compelling, also makes it especially difficult to study. Thus, in studies of aging, researchers have turned to non-human primate models, including chimpanzees, baboons, and rhesus macaques. More recently, the common marmoset, Callithrix jacchus, has been recognized as a particularly valuable model in studies of aging, given its small size, ease of housing in captivity, and relatively short lifespan. However, little is known about the physiological changes that occur as marmosets age. To begin to fill in this gap, we utilized high sensitivity metabolomics to define the longitudinal biochemical changes associated with age in the common marmoset. We measured 2104 metabolites from blood plasma at three separate time points over a 17-month period, and we completed both a cross-sectional and longitudinal analysis of the metabolome. We discovered hundreds of metabolites associated with age and body weight in both male and female animals. Our longitudinal analysis identified age-associated metabolic pathways that were not found in our cross-sectional analysis. Pathways enriched for age-associated metabolites included tryptophan, nucleotide, and xenobiotic metabolism, suggesting these biochemical pathways might play an important role in the basic mechanisms of aging in primates. Moreover, we found that many metabolic pathways associated with age were sex specific. Our work illustrates the power of longitudinal approaches, even in a short time frame, to discover novel biochemical changes that occur with age.
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Affiliation(s)
- Jessica M Hoffman
- Department of Genetics, University of Georgia, 120 Green Street, Athens, GA 30602, USA.
| | - ViLinh Tran
- Division of Pulmonary Allergy and Critical Care, Department of Medicine, Emory University, 615 Michael Street, Suite 225, Atlanta, GA 30322,USA; Clinical Biomarkers Laboratory, Department of Medicine, Emory University, 615 Michael Street, Suite 225, Atlanta, GA 30322,USA
| | - Lynn M Wachtman
- New England Primate Research Center, Harvard University, 1 Pinehill Rd, Southborough, MA 10772, USA
| | - Cara L Green
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, Scotland, UK
| | - Dean P Jones
- Division of Pulmonary Allergy and Critical Care, Department of Medicine, Emory University, 615 Michael Street, Suite 225, Atlanta, GA 30322,USA; Clinical Biomarkers Laboratory, Department of Medicine, Emory University, 615 Michael Street, Suite 225, Atlanta, GA 30322,USA
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Biology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
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32
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Marques AP, Serralheiro ML, Ferreira AEN, Freire AP, Cordeiro C, Silva MS. Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:38-54. [PMID: 26537432 DOI: 10.1002/bmb.20919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/11/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening approach to identify all the metabolites in a given biological system is called metabolic fingerprinting. Using high-resolution and high-mass accuracy mass spectrometry, large metabolome coverage, sensitivity, and specificity can be attained. Although the theoretical concepts of this methodology are usually provided in life-science programs, hands-on laboratory experiments are not usually accessible to undergraduate students. Even if the instruments are available, there are not simple laboratory protocols created specifically for teaching metabolomics. We designed a straightforward hands-on laboratory experiment to introduce students to this methodology, relating it to biochemical knowledge through metabolic pathway mapping of the identified metabolites. This study focuses on mitochondrial metabolomics since mitochondria have a well-known, medium-sized cellular sub-metabolome. These features facilitate both data processing and pathway mapping. In this experiment, students isolate mitochondria from potatoes, extract the metabolites, and analyze them by high-resolution mass spectrometry (using an FT-ICR mass spectrometer). The resulting mass list is submitted to an online program for metabolite identification, and compounds associated with mitochondrial pathways can be highlighted in a metabolic network map.
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Affiliation(s)
- Ana Patrícia Marques
- Centro De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Departamento De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Laboratório De FTICR E Espectrometria De Massa Estrutural, Faculdade De Ciencias, Universidade De Lisboa, Lisboa, 1749-016, Portugal
| | - Maria Luisa Serralheiro
- Centro De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Departamento De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Laboratório De FTICR E Espectrometria De Massa Estrutural, Faculdade De Ciencias, Universidade De Lisboa, Lisboa, 1749-016, Portugal
| | - António E N Ferreira
- Centro De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Departamento De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Laboratório De FTICR E Espectrometria De Massa Estrutural, Faculdade De Ciencias, Universidade De Lisboa, Lisboa, 1749-016, Portugal
| | - Ana Ponces Freire
- Centro De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Departamento De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Laboratório De FTICR E Espectrometria De Massa Estrutural, Faculdade De Ciencias, Universidade De Lisboa, Lisboa, 1749-016, Portugal
| | - Carlos Cordeiro
- Centro De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Departamento De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Laboratório De FTICR E Espectrometria De Massa Estrutural, Faculdade De Ciencias, Universidade De Lisboa, Lisboa, 1749-016, Portugal
| | - Marta Sousa Silva
- Centro De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Departamento De Química E Bioquímica, Faculdade De Ciências, Universidade De Lisboa, Lisboa, 1749-016, Portugal
- Laboratório De FTICR E Espectrometria De Massa Estrutural, Faculdade De Ciencias, Universidade De Lisboa, Lisboa, 1749-016, Portugal
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Abstract
The exposome is a complement to the genome that includes non-genetic causes of disease. Multiple definitions are available, with salient points being global inclusion of exposures and behaviors, and cumulative integration of associated biologic responses. As such, the concept is both refreshingly simple and dauntingly complex. This article reviews high-resolution metabolomics (HRM) as an affordable approach to routinely analyze samples for a broad spectrum of environmental chemicals and biologic responses. HRM has been successfully used in multiple exposome research paradigms and is suitable to implement in a prototype universal exposure surveillance system. Development of such a structure for systematic monitoring of environmental exposures is an important step toward sequencing the exposome because it builds upon successes of exposure science, naturally connects external exposure to body burden and partitions the exposome into workable components. Practical results would be repositories of quantitative data on chemicals according to geography and biology. This would support new opportunities for environmental health analysis and predictive modeling. Complementary approaches to hasten development of exposome theory and associated biologic response networks could include experimental studies with model systems, analysis of archival samples from longitudinal studies with outcome data and study of relatively short-lived animals, such as household pets (dogs and cats) and non-human primates (common marmoset). International investment and cooperation to sequence the human exposome will advance scientific knowledge and also provide an important foundation to control adverse environmental exposures to sustain healthy living spaces and improve prediction and management of disease.
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Go YM, Walker DI, Liang Y, Uppal K, Soltow QA, Tran V, Strobel F, Quyyumi AA, Ziegler TR, Pennell KD, Miller GW, Jones DP. Reference Standardization for Mass Spectrometry and High-resolution Metabolomics Applications to Exposome Research. Toxicol Sci 2015; 148:531-43. [PMID: 26358001 DOI: 10.1093/toxsci/kfv198] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The exposome is the cumulative measure of environmental influences and associated biological responses throughout the lifespan, including exposures from the environment, diet, behavior, and endogenous processes. A major challenge for exposome research lies in the development of robust and affordable analytic procedures to measure the broad range of exposures and associated biologic impacts occurring over a lifetime. Biomonitoring is an established approach to evaluate internal body burden of environmental exposures, but use of biomonitoring for exposome research is often limited by the high costs associated with quantification of individual chemicals. High-resolution metabolomics (HRM) uses ultra-high resolution mass spectrometry with minimal sample preparation to support high-throughput relative quantification of thousands of environmental, dietary, and microbial chemicals. HRM also measures metabolites in most endogenous metabolic pathways, thereby providing simultaneous measurement of biologic responses to environmental exposures. The present research examined quantification strategies to enhance the usefulness of HRM data for cumulative exposome research. The results provide a simple reference standardization protocol in which individual chemical concentrations in unknown samples are estimated by comparison to a concurrently analyzed, pooled reference sample with known chemical concentrations. The approach was tested using blinded analyses of amino acids in human samples and was found to be comparable to independent laboratory results based on surrogate standardization or internal standardization. Quantification was reproducible over a 13-month period and extrapolated to thousands of chemicals. The results show that reference standardization protocol provides an effective strategy that will enhance data collection for cumulative exposome research. In principle, the approach can be extended to other types of mass spectrometry and other analytical methods.
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Affiliation(s)
- Young-Mi Go
- *Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322
| | - Douglas I Walker
- *Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322; †Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts 02155
| | - Yongliang Liang
- *Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322
| | - Karan Uppal
- *Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322
| | - Quinlyn A Soltow
- *Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322
| | - ViLinh Tran
- *Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322
| | | | | | - Thomas R Ziegler
- Endocrinology, Metabolism and Lipids, Department of Medicine, Atlanta, Georgia 30322; and
| | - Kurt D Pennell
- †Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts 02155
| | - Gary W Miller
- Department of Environmental Health Sciences, Emory University, Atlanta, Georgia 30322
| | - Dean P Jones
- *Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322;
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Go YM, Kim CW, Walker DI, Kang DW, Kumar S, Orr M, Uppal K, Quyyumi AA, Jo H, Jones DP. Disturbed flow induces systemic changes in metabolites in mouse plasma: a metabolomics study using ApoE⁻/⁻ mice with partial carotid ligation. Am J Physiol Regul Integr Comp Physiol 2014; 308:R62-72. [PMID: 25377480 DOI: 10.1152/ajpregu.00278.2014] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Disturbed blood flow (d-flow) occurring in branched and curved arteries promotes endothelial dysfunction and atherosclerosis, in part, by altering gene expression and epigenomic profiles in endothelial cells. While a systemic metabolic change is known to play a role in atherosclerosis, it is unclear whether it can be regulated by local d-flow. Here, we tested this hypothesis by carrying out a metabolomics study using blood plasma samples obtained from ApoE(-/-) mice that underwent a partial carotid ligation surgery to induce d-flow. Mice receiving sham ligation were used as a control. To study early metabolic changes, samples collected from 1 wk after partial ligation when endothelial dysfunction occurs, but before atheroma develops, were analyzed by high-resolution mass spectrometry. A metabolome-wide association study showed that 128 metabolites were significantly altered in the ligated mice compared with the sham group. Of these, sphingomyelin (SM; m/z 703.5747), a common mammalian cell membrane sphingolipid, was most significantly increased in the ligated mice. Of the 128 discriminatory metabolites, 18 and 41 were positively and negatively correlated with SM, respectively. The amino acids methionine and phenylalanine were increased by d-flow, while phosphatidylcholine and phosphatidylethanolamine were decreased by d-flow, and these metabolites were correlated with SM. Other significantly affected metabolites included dietary and environmental agents. Pathway analysis showed that the metabolic changes of d-flow impacted broad functional networks. These results suggest that signaling from d-flow occurring in focal regions induces systemic metabolic changes associated with atherosclerosis.
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Affiliation(s)
- Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Chan Woo Kim
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Douglas I Walker
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia; Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts; and
| | - Dong Won Kang
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Sandeep Kumar
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Michael Orr
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Karan Uppal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Arshed A Quyyumi
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia
| | - Hanjoong Jo
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia;
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