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Xu K, Saaoud F, Shao Y, Lu Y, Wu S, Zhao H, Chen K, Vazquez-Padron R, Jiang X, Wang H, Yang X. Early hyperlipidemia triggers metabolomic reprogramming with increased SAH, increased acetyl-CoA-cholesterol synthesis, and decreased glycolysis. Redox Biol 2023; 64:102771. [PMID: 37364513 PMCID: PMC10310484 DOI: 10.1016/j.redox.2023.102771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
To identify metabolomic reprogramming in early hyperlipidemia, unbiased metabolome was screened in four tissues from ApoE-/- mice fed with high fat diet (HFD) for 3 weeks. 30, 122, 67, and 97 metabolites in the aorta, heart, liver, and plasma, respectively, were upregulated. 9 upregulated metabolites were uremic toxins, and 13 metabolites, including palmitate, promoted a trained immunity with increased syntheses of acetyl-CoA and cholesterol, increased S-adenosylhomocysteine (SAH) and hypomethylation and decreased glycolysis. The cross-omics analysis found upregulation of 11 metabolite synthetases in ApoE‾/‾ aorta, which promote ROS, cholesterol biosynthesis, and inflammation. Statistical correlation of 12 upregulated metabolites with 37 gene upregulations in ApoE‾/‾ aorta indicated 9 upregulated new metabolites to be proatherogenic. Antioxidant transcription factor NRF2-/- transcriptome analysis indicated that NRF2 suppresses trained immunity-metabolomic reprogramming. Our results have provided novel insights on metabolomic reprogramming in multiple tissues in early hyperlipidemia oriented toward three co-existed new types of trained immunity.
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Affiliation(s)
- Keman Xu
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Fatma Saaoud
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ying Shao
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Yifan Lu
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Sheng Wu
- Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Huaqing Zhao
- Medical Education and Data Science, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Kaifu Chen
- Computational Biology Program, Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Vazquez-Padron
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, 33125, USA
| | - Xiaohua Jiang
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Hong Wang
- Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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2
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Yu N, Wang R, Liu B, Zhang L. Bibliometric and Visual Analysis on Metabolomics in Coronary Artery Disease Research. Front Cardiovasc Med 2022; 9:804463. [PMID: 35402548 PMCID: PMC8990927 DOI: 10.3389/fcvm.2022.804463] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/28/2022] [Indexed: 12/13/2022] Open
Abstract
Background Metabolomics has immense research value in coronary artery disease and has drawn increasing attention over the past decades. Many articles have been published in this field, which may challenge researchers aiming to investigate all the available information. However, bibliometrics can provide deep insights into this research field. Objective We aimed to qualitatively and quantitatively study metabolomics and coronary artery disease research, visually analyse the development status, trends, research hotspots, and frontiers of this field, and provide a reference for research on coronary artery disease. Methods Articles were acquired from the Web of Science Core Collection. VOSviewer and CiteSpace software were used to analyse publication growth, country/region, institution, journal distribution, author, reference, and keywords, and detected the keywords with strong citation burstness to identify emerging topics. Results A total of 1121 references were obtained, and the annual number of publications increased over the past 16 years. Metabolomics research has shown a gradual upward trend in coronary artery disease. The United States of America and China ranked at the top in terms of percentage of articles. The institution with the highest number of research publications in this field was Harvard University, followed by the University of California System and Brigham Women's Hospital. The most frequently cited authors included Hazen SL, Tang WH, and Wang ZN. Ala-Korpela M was the most productive author, followed by Clish CB and Adamski J. The journal with the most publications in this field was Scientific Reports, followed by PLoS One and the Journal of Proteome Research. The keywords used at a high frequency were "risk," "biomarkers," "insulin resistance," and "atherosclerosis." Burst detection analysis of top keywords showed that "microbiota," "tryptophan," and "diabetes" are the current research frontiers in this field. Conclusion This study provides useful information for acquiring knowledge on metabolomics and coronary artery diseases. Metabolomics research has shown a gradual upward trend in coronary artery disease studies over the past 16 years. Research on tryptophan metabolism regulated by intestinal flora will become an emerging academic trend in this field, which can offer guidance for more extensive and in-depth studies in the future.
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Affiliation(s)
- Ning Yu
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ruirui Wang
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baocheng Liu
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lei Zhang
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Deng L, Fu D, Zhu L, Huang J, Ling Y, Cai Z. Testosterone deficiency accelerates early stage atherosclerosis in miniature pigs fed a high-fat and high-cholesterol diet: urine 1H NMR metabolomics targeted analysis. Mol Cell Biochem 2020; 476:1245-1255. [PMID: 33226572 DOI: 10.1007/s11010-020-03987-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/16/2020] [Indexed: 01/17/2023]
Abstract
To gain insights into the role of testosterone in the development of atherosclerosis and its related metabolic pathways, we applied a proton nuclear magnetic resonance (1H NMR)-based metabolomics approach to investigate urine metabolic profiles in miniature pigs fed a high-fat and high-cholesterol (HFC) diet among intact male pigs (IM), castrated male pigs (CM) and castrated male pigs with testosterone replacement (CMT). Our results showed that testosterone deficiency significantly increased atherosclerotic lesion areas, intima-media thickness, as well as serum lipid levels in the CM pigs. Moreover, seventeen significantly changed metabolites were identified in both IM vs. CM and CMT vs. CM groups. Among these, seven were shared between the two comparative groups and were all significantly reduced in the urine of the CM group but rescued in the CMT group. In addition, the correlation analysis demonstrated that several metabolites, including niacinamide, myo-inositol, choline and 3-hydroxyisovalerate, were negatively correlated with atherosclerotic lesion areas. Our study demonstrated that testosterone deficiency accelerated early AS formation in HFC diet-fed pigs, which involved several metabolites predominantly related to lipid metabolism, inflammation, oxidative stress and endothelial disorders. Our results reveal potential pathways in the pathogenesis of atherosclerosis caused by testosterone deficiency and HFC diet.
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Affiliation(s)
- Liqun Deng
- Laboratory Animal Research Center, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Danting Fu
- Laboratory Animal Research Center, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Department of Experimental Animals, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, 310012, China
| | - Liang Zhu
- Laboratory Animal Research Center, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Junjie Huang
- Laboratory Animal Research Center, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yun Ling
- Laboratory Animal Research Center, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Zhaowei Cai
- Laboratory Animal Research Center, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China. .,Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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4
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Zaric BL, Radovanovic JN, Gluvic Z, Stewart AJ, Essack M, Motwalli O, Gojobori T, Isenovic ER. Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes. Front Immunol 2020; 11:551758. [PMID: 33117340 PMCID: PMC7549398 DOI: 10.3389/fimmu.2020.551758] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/25/2020] [Indexed: 02/05/2023] Open
Abstract
Cardiovascular disease is the leading global health concern and responsible for more deaths worldwide than any other type of disorder. Atherosclerosis is a chronic inflammatory disease in the arterial wall, which underpins several types of cardiovascular disease. It has emerged that a strong relationship exists between alterations in amino acid (AA) metabolism and the development of atherosclerosis. Recent studies have reported positive correlations between levels of branched-chain amino acids (BCAAs) such as leucine, valine, and isoleucine in plasma and the occurrence of metabolic disturbances. Elevated serum levels of BCAAs indicate a high cardiometabolic risk. Thus, BCAAs may also impact atherosclerosis prevention and offer a novel therapeutic strategy for specific individuals at risk of coronary events. The metabolism of AAs, such as L-arginine, homoarginine, and L-tryptophan, is recognized as a critical regulator of vascular homeostasis. Dietary intake of homoarginine, taurine, and glycine can improve atherosclerosis by endothelium remodeling. Available data also suggest that the regulation of AA metabolism by indoleamine 2,3-dioxygenase (IDO) and arginases 1 and 2 are mediated through various immunological signals and that immunosuppressive AA metabolizing enzymes are promising therapeutic targets against atherosclerosis. Further clinical studies and basic studies that make use of animal models are required. Here we review recent data examining links between AA metabolism and the development of atherosclerosis.
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Affiliation(s)
- Bozidarka L. Zaric
- Department of Radiobiology and Molecular Genetics, “VINČA” Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jelena N. Radovanovic
- Department of Radiobiology and Molecular Genetics, “VINČA” Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Zoran Gluvic
- Department of Endocrinology and Diabetes, Faculty of Medicine, University Clinical-Hospital Centre Zemun-Belgrade, University of Belgrade, Belgrade, Serbia
| | - Alan J. Stewart
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olaa Motwalli
- College of Computing and Informatics, Saudi Electronic University (SEU), Medina, Saudi Arabia
| | - Takashi Gojobori
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Esma R. Isenovic
- Department of Radiobiology and Molecular Genetics, “VINČA” Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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The Active Compounds of Yixin Ningshen Tablet and Their Potential Action Mechanism in Treating Coronary Heart Disease- A Network Pharmacology and Proteomics Approach. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:4912395. [PMID: 32419806 PMCID: PMC7204378 DOI: 10.1155/2020/4912395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 09/15/2019] [Accepted: 10/10/2019] [Indexed: 12/22/2022]
Abstract
Yixin Ningshen tablet is a CFDA-approved TCM formula for treating coronary heart disease (CHD) clinically. However, its active compounds and mechanism of action in treating CHD are unknown. In this study, a novel strategy with the combination of network pharmacology and proteomics was proposed to identify the active components of Yixin Ningshen tablet and the mechanism by which they treat CHD. With the application of network pharmacology, 62 active compounds in Yixin Ningshen tablet were screened out by text mining, and their 313 potential target proteins were identified by a tool in SwissTargetPrediction. These data were integrated with known CHD-related proteomics results to predict the most possible targets, which reduced the 313 potential target proteins to 218. The STRING database was retrieved to find the enriched pathways and related diseases of these target proteins, which indicated that the Calcium, MAPK, PI3K-Akt, cAMP, Rap1, AGE-RAGE, Relaxin, HIF-1, Prolactin, Sphingolipid, Estrogen, IL-17, Jak-STAT signaling pathway, necroptosis, arachidonic acid metabolism, insulin resistance, endocrine resistance, and steroid hormone biosynthesis might be the main pathways regulated by Yixin Ningshen tablet for the treatment of CHD. Through further enrichment analysis and literature study, EGFR, ERBB2, VGFR2, FGF1, ESR1, LOX15, PGH2, HMDH, ADRB1, and ADRB2 were selected and then validated to be the target proteins of Yixin Ningshen tablet by molecular docking, which indicated that Yixin Ningshen tablet might treat CHD mainly through promoting heart regeneration, new vessels' formation, and the blood supply of the myocardial region and reducing cardiac output, oxygen demand, and inflammation as well as arteriosclerosis (promoting vasodilation and intraplaque neoangiogenesis, lowering blood lipid). This study is expected to benefit the clinical application of Yixin Ningshen tablet for the treatment of CHD.
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Myocardial metabolic alterations in mice with diet-induced atherosclerosis: linking sulfur amino acid and lipid metabolism. Sci Rep 2017; 7:13597. [PMID: 29051579 PMCID: PMC5648757 DOI: 10.1038/s41598-017-13991-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/04/2017] [Indexed: 02/08/2023] Open
Abstract
Atherosclerosis is a leading cause of cardiovascular disease (CVD), but the effect of diet on the atherosclerotic heart’s metabolism is unclear. We used an integrated metabolomics and lipidomics approach to evaluate metabolic perturbations in heart and serum from mice fed an atherogenic diet (AD) for 8, 16, and 25 weeks. Nuclear magnetic resonance (NMR)-based metabolomics revealed significant changes in sulfur amino acid (SAA) and lipid metabolism in heart from AD mice compared with heart from normal diet mice. Higher SAA levels in AD mice were quantitatively verified using liquid chromatography-mass spectrometry (LC/MS). Lipidomic profiling revealed that fatty acid and triglyceride (TG) levels in the AD group were altered depending on the degree of unsaturation. Additionally, levels of SCD1, SREBP-1, and PPARγ were reduced in AD mice after 25 weeks, while levels of reactive oxygen species were elevated. The results suggest that a long-term AD leads to SAA metabolism dysregulation and increased oxidative stress in the heart, causing SCD1 activity suppression and accumulation of toxic TGs with a low degree of unsaturation. These findings demonstrate that the SAA metabolic pathway is a promising therapeutic target for CVD treatment and that metabolomics can be used to investigate the metabolic signature of atherosclerosis.
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7
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Simmons RD, Kumar S, Thabet SR, Sur S, Jo H. Omics-based approaches to understand mechanosensitive endothelial biology and atherosclerosis. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:378-401. [PMID: 27341633 DOI: 10.1002/wsbm.1344] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 12/16/2022]
Abstract
Atherosclerosis is a multifactorial disease that preferentially occurs in arterial regions exposed to d-flow can be used to indicate disturbed flow or disturbed blood flow. The mechanisms by which d-flow induces atherosclerosis involve changes in the transcriptome, methylome, proteome, and metabolome of multiple vascular cells, especially endothelial cells. Initially, we begin with the pathogenesis of atherosclerosis and the changes that occur at multiple levels owing to d-flow, especially in the endothelium. Also, there are a variety of strategies used for the global profiling of the genome, transcriptome, miRNA-ome, DNA methylome, and metabolome that are important to define the biological and pathophysiological mechanisms of endothelial dysfunction and atherosclerosis. Finally, systems biology can be used to integrate these 'omics' datasets, especially those that derive data based on a single animal model, in order to better understand the pathophysiology of atherosclerosis development in a holistic manner and how this integrative approach could be used to identify novel molecular diagnostics and therapeutic targets to prevent or treat atherosclerosis. WIREs Syst Biol Med 2016, 8:378-401. doi: 10.1002/wsbm.1344 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Rachel D Simmons
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sandeep Kumar
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Salim Raid Thabet
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sanjoli Sur
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Hanjoong Jo
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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8
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Preclinical models of atherosclerosis. The future of Hybrid PET/MR technology for the early detection of vulnerable plaque. Expert Rev Mol Med 2016; 18:e6. [PMID: 27056676 DOI: 10.1017/erm.2016.5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cardiovascular diseases are the leading cause of death in developed countries. The aetiology is currently multifactorial, thus making them very difficult to prevent. Preclinical models of atherothrombotic diseases, including vulnerable plaque-associated complications, are now providing significant insights into pathologies like atherosclerosis, and in combination with the most recent advances in new non-invasive imaging technologies, they have become essential tools to evaluate new therapeutic strategies, with which can forecast and prevent plaque rupture. Positron emission tomography (PET)/computed tomography imaging is currently used for plaque visualisation in clinical and pre-clinical cardiovascular research, albeit with significant limitations. However, the combination of PET and magnetic resonance imaging (MRI) technologies is still the best option available today, as combined PET/MRI scans provide simultaneous data acquisition together with high quality anatomical information, sensitivity and lower radiation exposure for the patient. The coming years may represent a new era for the implementation of PET/MRI in clinical practice, but first, clinically efficient attenuation correction algorithms and research towards multimodal reagents and safety issues should be validated at the preclinical level.
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9
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The role of endothelial mechanosensitive genes in atherosclerosis and omics approaches. Arch Biochem Biophys 2015; 591:111-31. [PMID: 26686737 DOI: 10.1016/j.abb.2015.11.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/29/2015] [Accepted: 11/04/2015] [Indexed: 12/24/2022]
Abstract
Atherosclerosis is the leading cause of morbidity and mortality in the U.S., and is a multifactorial disease that preferentially occurs in regions of the arterial tree exposed to disturbed blood flow. The detailed mechanisms by which d-flow induces atherosclerosis involve changes in the expression of genes, epigenetic patterns, and metabolites of multiple vascular cells, especially endothelial cells. This review presents an overview of endothelial mechanobiology and its relation to the pathogenesis of atherosclerosis with special reference to the anatomy of the artery and the underlying fluid mechanics, followed by a discussion of a variety of experimental models to study the role of fluid mechanics and atherosclerosis. Various in vitro and in vivo models to study the role of flow in endothelial biology and pathobiology are discussed in this review. Furthermore, strategies used for the global profiling of the genome, transcriptome, miR-nome, DNA methylome, and metabolome, as they are important to define the biological and pathophysiological mechanisms of atherosclerosis. These "omics" approaches, especially those which derive data based on a single animal model, provide unprecedented opportunities to not only better understand the pathophysiology of atherosclerosis development in a holistic and integrative manner, but also to identify novel molecular and diagnostic targets.
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10
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Griffin JL, Wang X, Stanley E. Does our gut microbiome predict cardiovascular risk? A review of the evidence from metabolomics. ACTA ACUST UNITED AC 2015; 8:187-91. [PMID: 25691688 DOI: 10.1161/circgenetics.114.000219] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Millions of microbes are found in the human gut, and are collectively referred as the gut microbiota. Recent studies have estimated that the microbiota genome contains 100-fold more genes than the host genome. These microbiota contribute to digestion by processing energy substrates unutilized by the host, with about half of the total genome of the gut microbiota being related to central carbon and amino acid metabolism as well as the biosynthesis of secondary metabolites. Therefore, the gut microbiome and its interaction with the host influences many aspects of health and disease, including the composition of biofluids such as urine and blood plasma. Metabolomics is uniquely suited to capture these functional host-microbe interactions. This review aims at providing an overview of recent metabolomics evidence of gut microbiota-host metabolic interactions with a specific focus on cardiovascular disease and related aspects of the metabolic syndrome. Furthermore, the emphasis is given on the complexities of translating these metabolite signatures as potential clinical biomarkers, as the composition and activity of gut microbiome change with many factors, particularly with diet, with special reference to trimethylamine-oxide.
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Affiliation(s)
- Julian L Griffin
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom.
| | - Xinzhu Wang
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Stanley
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom
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11
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Tian F, Gu L, Si A, Yao Q, Zhang X, Zhao J, Hu D. The metabolomic study on atherosclerosis mice and its application in a traditional Chinese medicine Sishen granule. Biomed Chromatogr 2015; 30:969-75. [PMID: 26488619 DOI: 10.1002/bmc.3637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/14/2015] [Accepted: 10/19/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Feng Tian
- The branch of Shanghai First People's Hospital; Shanghai 200081 China
| | - Lei Gu
- Shanghai Jiaotong University Affiliated First People's Hospital; Shanghai 200080 China
| | - Aiyong Si
- Shanghai University of Traditional Chinese Medicine; Shanghai 201203 China
| | - Quanbao Yao
- The branch of Shanghai First People's Hospital; Shanghai 200081 China
| | - Xianwei Zhang
- The branch of Shanghai First People's Hospital; Shanghai 200081 China
| | - Jihui Zhao
- Shanghai University of Traditional Chinese Medicine; Shanghai 201203 China
| | - Daode Hu
- Shanghai Jiaotong University Affiliated First People's Hospital; Shanghai 200080 China
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12
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Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1007:140-8. [PMID: 26596842 DOI: 10.1016/j.jchromb.2015.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 02/05/2023]
Abstract
The intestinal microbiota and their metabolites are closely related to the formation of atherosclerosis (AS). In this study, a metabolomic approach based on the reversed-phase liquid chromatography/quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) platform was established to analyze the metabolic profiling of fecal extracts from AS mice model. The established metabolomic platform was also used for clearing the effective mechanism of a Traditional Chinese Medicine (TCM) named Sishen granule (SSKL). Totally, sixteen potential biomarkers in faeces of AS mice were identified and 5 of them could be reversed by SSKL. Through functional analysis of these biomarkers and the established network, lipid metabolism, cholesterol metabolism, energy cycle, and inflammation reaction were considered as the most relevant pathological changes in gastrointestinal tract of AS mice. The metabolomic study not only revealed the potential biomarkers in AS mice' faeces but also supplied a systematic view of the pathological changes in gastrointestinal metabolite in AS mice. This metabolomic study also demonstrated that SSKL had the therapeutic effectiveness on AS through partly reversing the lipid metabolism, inflammation and energy metabolism.
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13
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Identification of Reliable Components in Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS): a Data-Driven Approach across Metabolic Processes. Sci Rep 2015; 5:15710. [PMID: 26531245 PMCID: PMC4632111 DOI: 10.1038/srep15710] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/27/2015] [Indexed: 02/08/2023] Open
Abstract
There is an increasing need to use multivariate statistical methods for understanding biological functions, identifying the mechanisms of diseases, and exploring biomarkers. In addition to classical analyses such as hierarchical cluster analysis, principal component analysis, and partial least squares discriminant analysis, various multivariate strategies, including independent component analysis, non-negative matrix factorization, and multivariate curve resolution, have recently been proposed. However, determining the number of components is problematic. Despite the proposal of several different methods, no satisfactory approach has yet been reported. To resolve this problem, we implemented a new idea: classifying a component as “reliable” or “unreliable” based on the reproducibility of its appearance, regardless of the number of components in the calculation. Using the clustering method for classification, we applied this idea to multivariate curve resolution-alternating least squares (MCR-ALS). Comparisons between conventional and modified methods applied to proton nuclear magnetic resonance (1H-NMR) spectral datasets derived from known standard mixtures and biological mixtures (urine and feces of mice) revealed that more plausible results are obtained by the modified method. In particular, clusters containing little information were detected with reliability. This strategy, named “cluster-aided MCR-ALS,” will facilitate the attainment of more reliable results in the metabolomics datasets.
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Westrick R, Fredman G. Platelets: Context-Dependent Vascular Protectors or Mediators of Disease. Arterioscler Thromb Vasc Biol 2015; 35:e25-9. [PMID: 26109740 DOI: 10.1161/atvbaha.115.305898] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Randal Westrick
- From the Department of Biological Sciences, Oakland University, Rochester, MI (R.W.); and Department of Medicine, Columbia University, New York, NY (G.F.)
| | - Gabrielle Fredman
- From the Department of Biological Sciences, Oakland University, Rochester, MI (R.W.); and Department of Medicine, Columbia University, New York, NY (G.F.).
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Wang X, West JA, Murray AJ, Griffin JL. Comprehensive Metabolic Profiling of Age-Related Mitochondrial Dysfunction in the High-Fat-Fed ob/ob Mouse Heart. J Proteome Res 2015; 14:2849-62. [PMID: 25985803 DOI: 10.1021/acs.jproteome.5b00128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ectopic deposition of fat is thought to lead to lipotoxicity and has been associated with mitochondrial dysfunction and diabetic cardiomyopathy. We have measured mitochondrial respiratory capacities in the hearts of ob/ob and wild-type mice on either a regular chow (RCD) or high-fat (HFD) diet across four age groups to investigate the impact of diet and age on mitochondrial function alongside a comprehensive strategy for metabolic profiling of the tissue. Myocardial mitochondrial dysfunction was only evident in ob/ob mice on RCD at 14 months, but it was detectable at 3 months on the HFD. Liquid chromatography-mass spectrometry (LC-MS) was used to study the profiles of acylcarnitines and the accumulation of triglycerides, but neither class of lipid was associated with mitochondrial dysfunction. However, a targeted LC-MS/MS analysis of markers of oxidative stress demonstrated increases in GSSG/GSH and 8-oxoguanine, in addition to the accumulation of diacylglycerols, which are lipid species linked to lipotoxicity. Our results demonstrate that myocardial mitochondria in ob/ob mice on RCD maintained a similar respiratory capacity to that of wild type until a late stage in aging. However, on a HFD, unlike wild-type mice, ob/ob mice failed to increase mitochondrial respiration, which may be associated with a complex I defect following increased oxidative damage.
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Affiliation(s)
- Xinzhu Wang
- ‡MRC, Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, U.K
| | - James A West
- ‡MRC, Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, U.K
| | - Andrew J Murray
- §Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, U.K
| | - Julian L Griffin
- ‡MRC, Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, U.K
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Li AP, Li ZY, Sun HF, Li K, Qin XM, Du GH. Comparison of Two Different Astragali Radix by a ¹H NMR-Based Metabolomic Approach. J Proteome Res 2015; 14:2005-16. [PMID: 25844502 DOI: 10.1021/pr501167u] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Astragali Radix (AR) is a commonly used herbal drug in traditional chinese medicine and is widely used for the treatment of diabetes, cardiovascular diseases, nephropathy, and neuropathy. The main source of AR in China is the dried root of Astragalus membranaceus var. mongholicus (Bge.) Hsiao, and both cultivated and wild ARs are used clinically. A systematic comparison of cultivated AR (GS-AR) and wild AR (SX-AR) should be performed to ensure the clinical efficacy and safety. In this study, the chemical composition of the two different ARs, which were collected in the Shanxi (wild) and Gansu (cultivated) provinces, were compared by NMR-based metabolic fingerprint coupled with multivariate analysis. The SX-AR- and GS-AR-induced metabolic changes in the endogenous metabolites in mice were also compared. The results showed that SX-AR and GS-AR differed significantly not only in the primary metabolites but also in the secondary metabolites. However, alterations among the endogenous metabolites in the serum, lung, liver, and spleen were relatively small. This study provided a novel and valuable method for the evaluation of the consistency and diversity of herbal drugs, and further studies should be conducted on the difference in polysaccharides as well as the biological effects between the two kinds of AR.
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Affiliation(s)
| | | | | | | | | | - Guan-Hua Du
- §Institute of Materia Medica, Chinese Academy of Medical Sciences, Beijing 100050, People's Republic of China
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18
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Li D, Zhang L, Dong F, Liu Y, Li N, Li H, Lei H, Hao F, Wang Y, Zhu Y, Tang H. Metabonomic Changes Associated with Atherosclerosis Progression for LDLR(-/-) Mice. J Proteome Res 2015; 14:2237-54. [PMID: 25784267 DOI: 10.1021/acs.jproteome.5b00032] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Atherosclerosis resulting from hyperlipidemia causes many serious cardiovascular diseases. To understand the systems changes associated with pathogenesis and progression of atherosclerosis, we comprehensively analyzed the dynamic metabonomic changes in multiple biological matrices of LDLR(-/-) mice using NMR and GC-FID/MS with gene expression, clinical chemistry, and histopathological data as well. We found that 12 week "Western-type" diet (WD) treatment caused obvious aortic lesions, macrophage infiltration, and collagen level elevation in LDLR(-/-) mice accompanied by up-regulation of inflammatory factors including aortic ICAM-1, MCP-1, iNOS, MMP2, and hepatic TNFα and IL-1β. The WD-induced atherosclerosis progression was accompanied by metabonomic changes in multiple matrices including biofluids (plasma, urine) and (liver, kidney, myocardial) tissues involving multiple metabolic pathways. These included disruption of cholesterol homeostasis, disturbance of biosynthesis of amino acids and proteins, altered gut microbiota functions together with metabolisms of vitamin-B3, choline, purines, and pyrimidines. WD treatment caused down-regulation of SCD1 and promoted oxidative stress reflected by urinary allantoin elevation and decreases in hepatic PUFA-to-MUFA ratio. When switching to normal diet, atherosclerotic LDLR(-/-) mice reprogrammed their metabolisms and reversed the atherosclerosis-associated metabonomic changes to a large extent, although aortic lesions, inflammation parameters, macrophage infiltration, and collagen content were only partially alleviated. We concluded that metabolisms of fatty acids and vitamin-B3 together with gut microbiota played crucially important roles in atherosclerosis development. These findings offered essential biochemistry details of the diet-induced atherosclerosis and demonstrated effectiveness of the integrated metabonomic analysis of multiple biological matrices for understanding the molecular aspects of cardiovascular diseases.
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Affiliation(s)
- Dan Li
- †Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing 100191, China
| | - Lulu Zhang
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fangcong Dong
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yan Liu
- †Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing 100191, China
| | - Ning Li
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Huihui Li
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hehua Lei
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fuhua Hao
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yulan Wang
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China.,∥Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China
| | - Yi Zhu
- †Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing 100191, China.,⊥Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin 300070, China
| | - Huiru Tang
- ‡CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China.,§State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Metabonomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai 200433, China
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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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20
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Sun J, Monagas M, Jang S, Molokin A, Harnly JM, Urban JF, Solano-Aguilar G, Chen P. A high fat, high cholesterol diet leads to changes in metabolite patterns in pigs--a metabolomic study. Food Chem 2014; 173:171-8. [PMID: 25466009 DOI: 10.1016/j.foodchem.2014.09.161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/05/2014] [Accepted: 09/30/2014] [Indexed: 01/05/2023]
Abstract
Non-targeted metabolite profiling can identify biological markers of dietary exposure that lead to a better understanding of interactions between diet and health. In this study, pigs were used as an animal model to discover changes in metabolic profiles between regular basal and high fat/high cholesterol diets. Extracts of plasma, fecal and urine samples from pigs fed high fat or basal regular diets for 11 weeks were analysed using ultra-high performance liquid chromatography with high-resolution mass spectrometry (UHPLC-HRMS) and chemometric analysis. Cloud plots from XCMS online were used for class separation of the most discriminatory metabolites. The major metabolites contributing to the discrimination were identified as bile acids (BAs), lipid metabolites, fatty acids, amino acids and phosphatidic acid (PAs), phosphatidylglycerol (PGs), glycerophospholipids (PI), phosphatidylcholines (PCs) and tripeptides. These results suggest the developed approach can be used to identify biomarkers associated with specific feeding diets and possible metabolic disorders related to diet.
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Affiliation(s)
- Jianghao Sun
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Food Composition and Methods Development Laboratory, Beltsville, MD 20705, USA
| | - Maria Monagas
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, USA
| | - Saebyeol Jang
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, USA
| | - Aleksey Molokin
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, USA
| | - James M Harnly
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Food Composition and Methods Development Laboratory, Beltsville, MD 20705, USA
| | - Joseph F Urban
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, USA
| | - Gloria Solano-Aguilar
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, USA
| | - Pei Chen
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Food Composition and Methods Development Laboratory, Beltsville, MD 20705, USA.
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21
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Savorani F, Rasmussen MA, Mikkelsen MS, Engelsen SB. A primer to nutritional metabolomics by NMR spectroscopy and chemometrics. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.12.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Fardet A, Chardigny JM. Plant-Based Foods as a Source of Lipotropes for Human Nutrition: A Survey of In Vivo Studies. Crit Rev Food Sci Nutr 2013; 53:535-90. [DOI: 10.1080/10408398.2010.549596] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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23
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Jung JY, Kim IY, Kim YN, Kim JS, Shin JH, Jang ZH, Lee HS, Hwang GS, Seong JK. 1H NMR-based metabolite profiling of diet-induced obesity in a mouse mode. BMB Rep 2012; 45:419-24. [PMID: 22831978 DOI: 10.5483/bmbrep.2012.45.7.248] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
High-fat diets (HFD) and high-carbohydrate diets (HCD)- induced obesity through different pathways, but the metabolic differences between these diets are not fully understood. Therefore, we applied proton nuclear magnetic resonance ((1)H NMR)-based metabolomics to compare the metabolic patterns between C57BL/6 mice fed HCD and those fed HFD. Principal component analysis derived from (1)H NMR spectra of urine showed a clear separation between the HCD and HFD groups. Based on the changes in urinary metabolites, the slow rate of weight gain in mice fed the HCD related to activation of the tricarboxylic acid cycle (resulting in increased levels of citrate and succinate in HCD mice), while the HFD affected nicotinamide metabolism (increased levels of 1-methylnicotineamide, nicotinamide-N-oxide in HFD mice), which leads to systemic oxidative stress. In addition, perturbation of gut microflora metabolism was also related to different metabolic patterns of those two diets. These findings demonstrate that (1)H NMR-based metabolomics can identify diet-dependent perturbations in biological pathways.
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Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C. MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res 2012; 41:D781-6. [PMID: 23109552 PMCID: PMC3531110 DOI: 10.1093/nar/gks1004] [Citation(s) in RCA: 445] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.
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Affiliation(s)
- Kenneth Haug
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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25
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26
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Integration of metabolomics in heart disease and diabetes research: current achievements and future outlook. Bioanalysis 2011; 3:2205-22. [DOI: 10.4155/bio.11.223] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Abstract
Metabolomics represents a paradigm shift in metabolic research, away from approaches that focus on a limited number of enzymatic reactions or single pathways, to approaches that attempt to capture the complexity of metabolic networks. Additionally, the high-throughput nature of metabolomics makes it ideal to perform biomarker screens for diseases or follow drug efficacy. In this Review, we explore the role of metabolomics in gaining mechanistic insight into cardiac disease processes, and in the search for novel biomarkers. High-resolution NMR spectroscopy and mass spectrometry are both highly discriminatory for a range of pathological processes affecting the heart, including cardiac ischemia, myocardial infarction, and heart failure. We also discuss the position of metabolomics in the range of functional-genomic approaches, being complementary to proteomic and transcriptomic studies, and having subdivisions such as lipidomics (the study of intact lipid species). In addition to techniques that monitor changes in the total sizes of pools of metabolites in the heart and biofluids, the role of stable-isotope methods for monitoring fluxes through pathways is examined. The use of these novel functional-genomic tools to study metabolism provides a unique insight into cardiac disease progression.
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Affiliation(s)
- Julian L Griffin
- MRC Human Nutrition Research, Elsie Widdowson Laboratory, Fulbourn Road, Cambridge CB1 9NL, UK. jules.griffin@ mrc-hnr.cam.ac.uk
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Xiao X, Dawson N, MacIntyre L, Morris BJ, Pratt JA, Watson DG, Higham DJ. Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the Generalized Singular Value Decomposition. BMC SYSTEMS BIOLOGY 2011; 5:72. [PMID: 21575198 PMCID: PMC3239845 DOI: 10.1186/1752-0509-5-72] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 05/16/2011] [Indexed: 02/04/2023]
Abstract
BACKGROUND The quantification of experimentally-induced alterations in biological pathways remains a major challenge in systems biology. One example of this is the quantitative characterization of alterations in defined, established metabolic pathways from complex metabolomic data. At present, the disruption of a given metabolic pathway is inferred from metabolomic data by observing an alteration in the level of one or more individual metabolites present within that pathway. Not only is this approach open to subjectivity, as metabolites participate in multiple pathways, but it also ignores useful information available through the pairwise correlations between metabolites. This extra information may be incorporated using a higher-level approach that looks for alterations between a pair of correlation networks. In this way experimentally-induced alterations in metabolic pathways can be quantitatively defined by characterizing group differences in metabolite clustering. Taking this approach increases the objectivity of interpreting alterations in metabolic pathways from metabolomic data. RESULTS We present and justify a new technique for comparing pairs of networks--in our case these networks are based on the same set of nodes and there are two distinct types of weighted edges. The algorithm is based on the Generalized Singular Value Decomposition (GSVD), which may be regarded as an extension of Principle Components Analysis to the case of two data sets. We show how the GSVD can be interpreted as a technique for reordering the two networks in order to reveal clusters that are exclusive to only one. Here we apply this algorithm to a new set of metabolomic data from the prefrontal cortex (PFC) of a translational model relevant to schizophrenia, rats treated subchronically with the N-methyl-D-Aspartic acid (NMDA) receptor antagonist phencyclidine (PCP). This provides us with a means to quantify which predefined metabolic pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolite pathway database) were altered in the PFC of PCP-treated rats. Several significant changes were discovered, notably: 1) neuroactive ligands active at glutamate and GABA receptors are disrupted in the PFC of PCP-treated animals, 2) glutamate dysfunction in these animals was not limited to compromised glutamatergic neurotransmission but also involves the disruption of metabolic pathways linked to glutamate; and 3) a specific series of purine reactions Xanthine ← Hypoxyanthine ↔ Inosine ← IMP → adenylosuccinate is also disrupted in the PFC of PCP-treated animals. CONCLUSIONS Network reordering via the GSVD provides a means to discover statistically validated differences in clustering between a pair of networks. In practice this analytical approach, when applied to metabolomic data, allows us to quantify the alterations in metabolic pathways between two experimental groups. With this new computational technique we identified metabolic pathway alterations that are consistent with known results. Furthermore, we discovered disruption in a novel series of purine reactions that may contribute to the PFC dysfunction and cognitive deficits seen in schizophrenia.
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Affiliation(s)
- Xiaolin Xiao
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, G1 1XH, Scotland, UK
| | - Neil Dawson
- Psychiatric Research Institute of Neuroscience in Glasgow (PsyRING), Universities of Glasgow and Strathclyde, G12 8QQ, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow, G4 0NR, UK
- Center for Neuroscience, University of Strathclyde (CeNsUS), Glasgow, G4 0NR, UK
| | - Lynsey MacIntyre
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow, G4 0NR, UK
| | - Brian J Morris
- Psychiatric Research Institute of Neuroscience in Glasgow (PsyRING), Universities of Glasgow and Strathclyde, G12 8QQ, UK
- Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Judith A Pratt
- Psychiatric Research Institute of Neuroscience in Glasgow (PsyRING), Universities of Glasgow and Strathclyde, G12 8QQ, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow, G4 0NR, UK
- Center for Neuroscience, University of Strathclyde (CeNsUS), Glasgow, G4 0NR, UK
| | - David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow, G4 0NR, UK
- Center for Neuroscience, University of Strathclyde (CeNsUS), Glasgow, G4 0NR, UK
| | - Desmond J Higham
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, G1 1XH, Scotland, UK
- Center for Neuroscience, University of Strathclyde (CeNsUS), Glasgow, G4 0NR, UK
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Abonnenc M, Stegemann C, Mayr M. Highlights from the 2010 BAS/BSCR spring meeting: New Frontiers in Cardiovascular Research. Expert Rev Proteomics 2010; 7:811-3. [PMID: 21142882 DOI: 10.1586/epr.10.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The British Atherosclerosis Society (BAS)/British Society for Cardiovascular Research (BSCR) spring meeting was held in Manchester, UK, on 7-8 June 2010. Experts in the field of systems biology, proteomics, metabolomics and miRNAs presented how these techniques can be used to discover 'New Frontiers in Cardiovascular Research'. The conference was attended by over 150 participants, mainly from the UK. A total of 2 days of presentations and a poster session with 55 posters provided the possibility to discuss the latest research results and showed the opportunities that new techniques can offer in cardiovascular research.
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Affiliation(s)
- Mélanie Abonnenc
- King's BHF Centre, King's College London, 125 Coldharbour Lane, London, UK
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30
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Kirwan GM, Diez D, Haeggström JZ, Goto S, Wheelock CE. Systems Biology Approaches for Investigating the Relationship Between Lipids and Cardiovascular Disease. CURRENT CARDIOVASCULAR RISK REPORTS 2010. [DOI: 10.1007/s12170-010-0144-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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31
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Kim YS, Milner JA. Bioactive food components and cancer-specific metabonomic profiles. J Biomed Biotechnol 2010; 2011:721213. [PMID: 21113295 PMCID: PMC2989380 DOI: 10.1155/2011/721213] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 09/29/2010] [Accepted: 10/05/2010] [Indexed: 02/07/2023] Open
Abstract
Cancer cells possess unique metabolic signatures compared to normal cells, including shifts in aerobic glycolysis, glutaminolysis, and de novo biosynthesis of macromolecules. Targeting these changes with agents (drugs and dietary components) has been employed as strategies to reduce the complications associated with tumorigenesis. This paper highlights the ability of several food components to suppress tumor-specific metabolic pathways, including increased expression of glucose transporters, oncogenic tyrosine kinase, tumor-specific M2-type pyruvate kinase, and fatty acid synthase, and the detection of such effects using various metabonomic technologies, including liquid chromatography/mass spectrometry (LC/MS) and stable isotope-labeled MS. Stable isotope-mediated tracing technologies offer exciting opportunities for defining specific target(s) for food components. Exposures, especially during the early transition phase from normal to cancer, are critical for the translation of knowledge about food components into effective prevention strategies. Although appropriate dietary exposures needed to alter cellular metabolism remain inconsistent and/or ill-defined, validated metabonomic biomarkers for dietary components hold promise for establishing effective strategies for cancer prevention.
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Affiliation(s)
- Young S. Kim
- Nutritional Science Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John A. Milner
- Nutritional Science Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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