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Li R, Shao Y, Yu Y, Wang X, Guo G. Pico-HPLC system integrating an equal inner diameter femtopipette into a 900 nm I.D. porous layer open tubular column. Chem Commun (Camb) 2017; 53:4104-4107. [DOI: 10.1039/c7cc00799j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A pico-HPLC method was developed using a bifunctional chromatographic column enabling femtoliter volume sampling and separation.
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Affiliation(s)
- Ruonan Li
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Yunlong Shao
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Yanmin Yu
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Xiayan Wang
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Guangsheng Guo
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
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52
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Bhute VJ, Ma Y, Bao X, Palecek SP. The Poly (ADP-Ribose) Polymerase Inhibitor Veliparib and Radiation Cause Significant Cell Line Dependent Metabolic Changes in Breast Cancer Cells. Sci Rep 2016; 6:36061. [PMID: 27811964 PMCID: PMC5095763 DOI: 10.1038/srep36061] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022] Open
Abstract
Breast tumors are characterized into subtypes based on their surface marker expression, which affects their prognosis and treatment. Poly (ADP-ribose) polymerase (PARP) inhibitors have shown promising results in clinical trials, both as single agents and in combination with other chemotherapeutics, in several subtypes of breast cancer patients. Here, we used NMR-based metabolomics to probe cell line-specific effects of the PARP inhibitor Veliparib and radiation on metabolism in three breast cancer cell lines. Our data reveal several cell line-independent metabolic changes upon PARP inhibition. Pathway enrichment and topology analysis identified that nitrogen metabolism, glycine, serine and threonine metabolism, aminoacyl-tRNA biosynthesis and taurine and hypotaurine metabolism were enriched after PARP inhibition in all three breast cancer cell lines. Many metabolic changes due to radiation and PARP inhibition were cell line-dependent, highlighting the need to understand how these treatments affect cancer cell response via changes in metabolism. Finally, both PARP inhibition and radiation induced a similar metabolic responses in BRCA-mutant HCC1937 cells, but not in MCF7 and MDAMB231 cells, suggesting that radiation and PARP inhibition share similar interactions with metabolic pathways in BRCA mutant cells. Our study emphasizes the importance of differences in metabolic responses to cancer treatments in different subtypes of cancers.
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Affiliation(s)
- Vijesh J Bhute
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yan Ma
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaoping Bao
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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53
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Zhao S, Luo X, Li L. Chemical Isotope Labeling LC-MS for High Coverage and Quantitative Profiling of the Hydroxyl Submetabolome in Metabolomics. Anal Chem 2016; 88:10617-10623. [DOI: 10.1021/acs.analchem.6b02967] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Xian Luo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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54
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Huang JH, Berkovitch SS, Iaconelli J, Watmuff B, Park H, Chattopadhyay S, McPhie D, Öngür D, Cohen BM, Clish CB, Karmacharya R. Perturbational Profiling of Metabolites in Patient Fibroblasts Implicates α-Aminoadipate as a Potential Biomarker for Bipolar Disorder. MOLECULAR NEUROPSYCHIATRY 2016; 2:97-106. [PMID: 27606323 DOI: 10.1159/000446654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 05/04/2016] [Indexed: 12/27/2022]
Abstract
Many studies suggest the presence of aberrations in cellular metabolism in bipolar disorder. We studied the metabolome in bipolar disorder to gain insight into cellular pathways that may be dysregulated in bipolar disorder and to discover evidence of novel biomarkers. We measured polar and nonpolar metabolites in fibroblasts from subjects with bipolar I disorder and matched healthy control subjects, under normal conditions and with two physiologic perturbations: low-glucose media and exposure to the stress-mediating hormone dexamethasone. Metabolites that were significantly different between bipolar and control subjects showed distinct separation by principal components analysis methods. The most statistically significant findings were observed in the perturbation experiments. The metabolite with the lowest p value in both the low-glucose and dexamethasone experiments was α-aminoadipate, whose intracellular level was consistently lower in bipolar subjects. Our study implicates α-aminoadipate as a possible biomarker in bipolar disorder that manifests under cellular stress. This is an intriguing finding given the known role of α-aminoadipate in the modulation of kynurenic acid in the brain, especially as abnormal kynurenic acid levels have been implicated in bipolar disorder.
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Affiliation(s)
- Joanne H Huang
- Center for Experimental Drugs and Diagnostics, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Harvard Medical School and Massachusetts General Hospital, Boston, Mass., USA; Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA
| | - Shaunna S Berkovitch
- Center for Experimental Drugs and Diagnostics, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Harvard Medical School and Massachusetts General Hospital, Boston, Mass., USA; Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA
| | - Jonathan Iaconelli
- Center for Experimental Drugs and Diagnostics, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Harvard Medical School and Massachusetts General Hospital, Boston, Mass., USA; Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA
| | - Bradley Watmuff
- Center for Experimental Drugs and Diagnostics, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Harvard Medical School and Massachusetts General Hospital, Boston, Mass., USA; Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA
| | - Hyoungjun Park
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Mass., USA
| | - Shrikanta Chattopadhyay
- MGH Cancer Center, Boston, Mass., USA; Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA
| | - Donna McPhie
- Schizophrenia and Bipolar Disorder Program, Harvard Medical School and McLean Hospital, Belmont, Mass., USA
| | - Dost Öngür
- Schizophrenia and Bipolar Disorder Program, Harvard Medical School and McLean Hospital, Belmont, Mass., USA
| | - Bruce M Cohen
- Schizophrenia and Bipolar Disorder Program, Harvard Medical School and McLean Hospital, Belmont, Mass., USA
| | - Clary B Clish
- Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA
| | - Rakesh Karmacharya
- Center for Experimental Drugs and Diagnostics, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Harvard Medical School and Massachusetts General Hospital, Boston, Mass., USA; Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA; Chemical Biology Program, Broad Institute of Harvard and MIT, Mass., USA
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55
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Filla LA, Sanders KL, Filla RT, Edwards JL. Automated sample preparation in a microfluidic culture device for cellular metabolomics. Analyst 2016; 141:3858-65. [PMID: 27118418 PMCID: PMC4902300 DOI: 10.1039/c6an00237d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sample pretreatment in conventional cellular metabolomics entails rigorous lysis and extraction steps which increase the duration as well as limit the consistency of these experiments. We report a biomimetic cell culture microfluidic device (MFD) which is coupled with an automated system for rapid, reproducible cell lysis using a combination of electrical and chemical mechanisms. In-channel microelectrodes were created using facile fabrication methods, enabling the application of electric fields up to 1000 V cm(-1). Using this platform, average lysing times were 7.12 s and 3.03 s for chips with no electric fields and electric fields above 200 V cm(-1), respectively. Overall, the electroporation MFDs yielded a ∼10-fold improvement in lysing time over standard chemical approaches. Detection of multiple intracellular nucleotides and energy metabolites in MFD lysates was demonstrated using two different MS platforms. This work will allow for the integrated culture, automated lysis, and metabolic analysis of cells in an MFD which doubles as a biomimetic model of the vasculature.
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Affiliation(s)
- Laura A Filla
- Department of Chemistry, Saint Louis University, St Louis, MO 63130, USA.
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56
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Metabolic reprogramming through fatty acid transport protein 1 (FATP1) regulates macrophage inflammatory potential and adipose inflammation. Mol Metab 2016; 5:506-526. [PMID: 27408776 PMCID: PMC4921943 DOI: 10.1016/j.molmet.2016.04.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/08/2016] [Accepted: 04/18/2016] [Indexed: 12/22/2022] Open
Abstract
Objective A novel approach to regulate obesity-associated adipose inflammation may be through metabolic reprogramming of macrophages (MΦs). Broadly speaking, MΦs dependent on glucose are pro-inflammatory, classically activated MΦs (CAM), which contribute to adipose inflammation and insulin resistance. In contrast, MΦs that primarily metabolize fatty acids are alternatively activated MΦs (AAM) and maintain tissue insulin sensitivity. In actuality, there is much flexibility and overlap in the CAM-AAM spectrum in vivo dependent upon various stimuli in the microenvironment. We hypothesized that specific lipid trafficking proteins, e.g. fatty acid transport protein 1 (FATP1), would direct MΦ fatty acid transport and metabolism to limit inflammation and contribute to the maintenance of adipose tissue homeostasis. Methods Bone marrow derived MΦs (BMDMs) from Fatp1−/− and Fatp1+/+ mice were used to investigate FATP1-dependent substrate metabolism, bioenergetics, metabolomics, and inflammatory responses. We also generated C57BL/6J chimeric mice by bone marrow transplant specifically lacking hematopoetic FATP1 (Fatp1B−/−) and controls Fatp1B+/+. Mice were challenged by high fat diet (HFD) or low fat diet (LFD) and analyses including MRI, glucose and insulin tolerance tests, flow cytometric, histologic, and protein quantification assays were conducted. Finally, an FATP1-overexpressing RAW 264.7 MΦ cell line (FATP1-OE) and empty vector control (FATP1-EV) were developed as a gain of function model to test effects on substrate metabolism, bioenergetics, metabolomics, and inflammatory responses. Results Fatp1 is downregulated with pro-inflammatory stimulation of MΦs. Fatp1−/− BMDMs and FATP1-OE RAW 264.7 MΦs demonstrated that FATP1 reciprocally controled metabolic flexibility, i.e. lipid and glucose metabolism, which was associated with inflammatory response. Supporting our previous work demonstrating the positive relationship between glucose metabolism and inflammation, loss of FATP1 enhanced glucose metabolism and exaggerated the pro-inflammatory CAM phenotype. Fatp1B−/− chimeras fed a HFD gained more epididymal white adipose mass, which was inflamed and oxidatively stressed, compared to HFD-fed Fatp1B+/+ controls. Adipose tissue macrophages displayed a CAM-like phenotype in the absence of Fatp1. Conversely, functional overexpression of FATP1 decreased many aspects of glucose metabolism and diminished CAM-stimulated inflammation in vitro. FATP1 displayed acyl-CoA synthetase activity for long chain fatty acids in MΦs and modulated lipid mediator metabolism in MΦs. Conclusion Our findings provide evidence that FATP1 is a novel regulator of MΦ activation through control of substrate metabolism. Absence of FATP1 exacerbated pro-inflammatory activation in vitro and increased local and systemic components of the metabolic syndrome in HFD-fed Fatp1B−/− mice. In contrast, gain of FATP1 activity in MΦs suggested that Fatp1-mediated activation of fatty acids, substrate switch to glucose, oxidative stress, and lipid mediator synthesis are potential mechanisms. We demonstrate for the first time that FATP1 provides a unique mechanism by which the inflammatory tone of adipose and systemic metabolism may be regulated. FATP1-mediated activation of fatty acids is a novel approach to limit inflammation. Fatp1 deficiency primed macrophages for pro-inflammatory activation. Lack of Fatp1 led to greater HFD-induced adipose inflammation. Fatp1−/− adipose tissue macrophages were classically activated.
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Abstract
With a global prevalence of 9%, diabetes is the direct cause of millions of deaths each year and is quickly becoming a health crisis. Major long-term complications of diabetes arise from persistent oxidative stress and dysfunction in multiple metabolic pathways. The most serious complications involve vascular damage and include cardiovascular disease as well as microvascular disorders such as nephropathy, neuropathy, and retinopathy. Current clinical analyses like glycated hemoglobin and plasma glucose measurements hold some value as prognostic indicators of the severity of complications, but investigations into the underlying pathophysiology are still lacking. Advancements in biotechnology hold the key to uncovering new pathways and establishing therapeutic targets. Metabolomics, the study of small endogenous molecules, is a powerful toolset for studying pathophysiological processes and has been used to elucidate metabolic signatures of diabetes in various biological systems. Current challenges in the field involve correlating these biomarkers to specific complications to provide a better prediction of future risk and disease progression. This review will highlight the progress that has been made in the field of metabolomics including technological advancements, the identification of potential biomarkers, and metabolic pathways relevant to macro- and microvascular diabetic complications.
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Affiliation(s)
- Laura A Filla
- Saint Louis University Department of Chemistry, 3501 Laclede Ave. St. Louis, MO 63103, USA.
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58
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Yang S, Wang M, Chen L, Yin B, Song G, Turko IV, Phinney KW, Betenbaugh MJ, Zhang H, Li S. QUANTITY: An Isobaric Tag for Quantitative Glycomics. Sci Rep 2015; 5:17585. [PMID: 26616285 PMCID: PMC4663469 DOI: 10.1038/srep17585] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022] Open
Abstract
Glycan is an important class of macromolecules that play numerous biological functions. Quantitative glycomics - analysis of glycans at global level - however, is far behind genomics and proteomics owing to technical challenges associated with their chemical properties and structural complexity. As a result, technologies that can facilitate global glycan analysis are highly sought after. Here, we present QUANTITY (Quaternary Amine Containing Isobaric Tag for Glycan), a quantitative approach that can not only enhance detection of glycans by mass spectrometry, but also allow high-throughput glycomic analysis from multiple biological samples. This robust tool enabled us to accomplish glycomic survey of bioengineered Chinese Hamster Ovary (CHO) cells with knock-in/out enzymes involved in protein glycosylation. Our results demonstrated QUANTITY is an invaluable technique for glycan analysis and bioengineering.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Meiyao Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA.,Analytical Biotechnology, MedImmune LLC, Gaithersburg, MD, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Bojiao Yin
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guoqiang Song
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Illarion V Turko
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA.,Biomolecular Measurement Division, National Institute of Standard and Technology, Gaithersburg, MD, USA
| | - Karen W Phinney
- Biomolecular Measurement Division, National Institute of Standard and Technology, Gaithersburg, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA
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The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research. Methods Mol Biol 2015; 1277:161-93. [PMID: 25677154 DOI: 10.1007/978-1-4939-2377-9_13] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have evolved as the most common techniques in metabolomics studies, and each brings its own advantages and limitations. Unlike MS spectrometry, NMR spectroscopy is quantitative and does not require extra steps for sample preparation, such as separation or derivatization. Although the sensitivity of NMR spectroscopy has increased enormously and improvements continue to emerge steadily, this remains a weak point for NMR compared with MS. MS-based metabolomics provides an excellent approach that can offer a combined sensitivity and selectivity platform for metabolomics research. Moreover, different MS approaches such as different ionization techniques and mass analyzer technology can be used in order to increase the number of metabolites that can be detected. In this chapter, the advantages, limitations, strengths, and weaknesses of NMR and MS as tools applicable to metabolomics research are highlighted.
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60
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Li Z, Tatlay J, Li L. Nanoflow LC–MS for High-Performance Chemical Isotope Labeling Quantitative Metabolomics. Anal Chem 2015; 87:11468-74. [DOI: 10.1021/acs.analchem.5b03209] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhendong Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
| | - Jaspaul Tatlay
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
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61
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Wagner M, Ohlund LB, Shiao TC, Vézina A, Annabi B, Roy R, Sleno L. Isotope-labeled differential profiling of metabolites using N-benzoyloxysuccinimide derivatization coupled to liquid chromatography/high-resolution tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1632-1640. [PMID: 26467115 DOI: 10.1002/rcm.7264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/15/2015] [Accepted: 06/21/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE An isotopic labeling strategy based on derivatizing amine-containing metabolites has been developed using light ((12) C6 ) and heavy ((13) C6 ) N-benzoyloxysuccinimide reagents for semi-targeted metabolomic applications. METHODS Differentially labeled samples were combined and analyzed simultaneously by liquid chromatography/high-resolution tandem mass spectrometry (LC/HR-MS/MS) to compare relative amounts of amine-containing metabolites. The selectivity of the reaction was determined with model metabolites and was shown to also be applicable to thiol and phenol moieties. The potential for relative quantitation was evaluated in cell extracts and the method was then applied to quantify metabolic perturbations occurring in human cultured cells under normal vs. oxidative stress conditions. RESULTS A total of 279 derivatized features were detected in HL60 cell extracts, 77 of which yielded significant concentration changes upon oxidative stress treatment. Based on accurate mass measurements and MS/MS spectral matching with reference standard solutions, 10 metabolites were clearly identified. Derivatized compounds were found to have diagnostic fragment ions from the reagent itself, as well as structurally informative ions useful for metabolite identification. CONCLUSIONS This simple derivatization reaction can be applied to the relative quantitation of amine-, thiol- and phenol-containing compounds, with improved sensitivity and chromatographic peak shapes due to the increased hydrophobicity of polar metabolites not readily amenable to reversed-phase LC/MS analysis.
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Affiliation(s)
- Michel Wagner
- Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montréal, QC, Canada
| | - Leanne B Ohlund
- Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montréal, QC, Canada
| | - Tze Chieh Shiao
- Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montréal, QC, Canada
| | - Amélie Vézina
- Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montréal, QC, Canada
| | - Borhane Annabi
- Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montréal, QC, Canada
| | - René Roy
- Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montréal, QC, Canada
| | - Lekha Sleno
- Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montréal, QC, Canada
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Huan T, Wu Y, Tang C, Lin G, Li L. DnsID in MyCompoundID for rapid identification of dansylated amine- and phenol-containing metabolites in LC-MS-based metabolomics. Anal Chem 2015; 87:9838-45. [PMID: 26327437 DOI: 10.1021/acs.analchem.5b02282] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
High-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) is an enabling technology based on rational design of labeling reagents to target a class of metabolites sharing the same functional group (e.g., all the amine-containing metabolites or the amine submetabolome) to provide concomitant improvements in metabolite separation, detection, and quantification. However, identification of labeled metabolites remains to be an analytical challenge. In this work, we describe a library of labeled standards and a search method for metabolite identification in CIL LC-MS. The current library consists of 273 unique metabolites, mainly amines and phenols that are individually labeled by dansylation (Dns). Some of them produced more than one Dns-derivative (isomers or multiple labeled products), resulting in a total of 315 dansyl compounds in the library. These metabolites cover 42 metabolic pathways, allowing the possibility of probing their changes in metabolomics studies. Each labeled metabolite contains three searchable parameters: molecular ion mass, MS/MS spectrum, and retention time (RT). To overcome RT variations caused by experimental conditions used, we have developed a calibration method to normalize RTs of labeled metabolites using a mixture of RT calibrants. A search program, DnsID, has been developed in www.MyCompoundID.org for automated identification of dansyl labeled metabolites in a sample based on matching one or more of the three parameters with those of the library standards. Using human urine as an example, we illustrate the workflow and analytical performance of this method for metabolite identification. This freely accessible resource is expandable by adding more amine and phenol standards in the future. In addition, the same strategy should be applicable for developing other labeled standards libraries to cover different classes of metabolites for comprehensive metabolomics using CIL LC-MS.
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Affiliation(s)
- Tao Huan
- Departments of Chemistry and ‡Computing Science, University of Alberta , Edmonton, Alberta T6G2G2, Canada
| | - Yiman Wu
- Departments of Chemistry and ‡Computing Science, University of Alberta , Edmonton, Alberta T6G2G2, Canada
| | - Chenqu Tang
- Departments of Chemistry and ‡Computing Science, University of Alberta , Edmonton, Alberta T6G2G2, Canada
| | - Guohui Lin
- Departments of Chemistry and ‡Computing Science, University of Alberta , Edmonton, Alberta T6G2G2, Canada
| | - Liang Li
- Departments of Chemistry and ‡Computing Science, University of Alberta , Edmonton, Alberta T6G2G2, Canada
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63
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Yuan W, Li S, Edwards JL. Extraction and Quantitation of Ketones and Aldehydes from Mammalian Cells Using Fluorous Tagging and Capillary LC-MS. Anal Chem 2015; 87:7660-6. [DOI: 10.1021/acs.analchem.5b01000] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Wei Yuan
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States,
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Shuwei Li
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States,
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - James L. Edwards
- Department
of Chemistry, Saint Louis University, St. Louis, Missouri 63103, United States
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Huan T, Li L. Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry. Anal Chem 2015; 87:7011-6. [DOI: 10.1021/acs.analchem.5b01434] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tao Huan
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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65
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Zhou R, Huan T, Li L. Development of versatile isotopic labeling reagents for profiling the amine submetabolome by liquid chromatography–mass spectrometry. Anal Chim Acta 2015; 881:107-16. [DOI: 10.1016/j.aca.2015.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/06/2015] [Accepted: 04/11/2015] [Indexed: 01/09/2023]
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Abstract
Diabetes is characterized by altered metabolism of key molecules and regulatory pathways. The phenotypic expression of diabetes and associated complications encompasses complex interactions between genetic, environmental, and tissue-specific factors that require an integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate small molecule metabolites from biological systems. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled identification of complex metabolic phenotypes. Continued development of bioinformatics and analytical strategies has facilitated the discovery of causal links in understanding the pathophysiology of diabetes and its complications. Here, we summarize the metabolomics workflow, including analytical, statistical, and computational tools, highlight recent applications of metabolomics in diabetes research, and discuss the challenges in the field.
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Affiliation(s)
- Kelli M Sas
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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Filla LA, Yuan W, Feldman EL, Li S, Edwards JL. Global metabolomic and isobaric tagging capillary liquid chromatography-tandem mass spectrometry approaches for uncovering pathway dysfunction in diabetic mouse aorta. J Proteome Res 2014; 13:6121-34. [PMID: 25368974 PMCID: PMC4261973 DOI: 10.1021/pr501030e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Despite the prevalence of diabetes and the global health risks it poses, the biochemical pathogenesis of diabetic complications remains poorly understood with few effective therapies. This study employs capillary liquid chromatography (capLC) and tandem mass spectrometry (MS/MS) in conjunction with both global metabolomics and isobaric tags specific to amines and carbonyls to probe aortic metabolic content in diabetic mice with hyperglycemia, hyperlipidemia, hypertension, and stenotic vascular damage. Using these combined techniques, metabolites well-characterized in diabetes as well as novel pathways were investigated. A total of 53,986 features were detected, 719 compounds were identified as having significant fold changes (thresholds ≥ 2 or ≤ 0.5), and 48 metabolic pathways were found to be altered with at least 2 metabolite hits in diabetic samples. Pathways related to carbonyl stress, carbohydrate metabolism, and amino acid metabolism showed the greatest number of metabolite changes. Three novel pathways with previously limited or undescribed roles in diabetic complications--vitamin B6, propanoate, and butanoate metabolism--were also shown to be altered in multiple points along the pathway. These discoveries support the theory that diabetic vascular complications arise from the interplay of a myriad of metabolic pathways in conjunction with oxidative and carbonyl stress, which may provide not only new and much needed biomarkers but also insights into novel therapeutic targets.
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Affiliation(s)
- Laura A Filla
- Department of Chemistry, Saint Louis University , St. Louis, Missouri 63103, United States
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Yang H, Lin W, Zhang J, Lin W, Xu P, Li J, Ling X. Metabonomic analysis of the toxic effects of TM208 in rat urine by HPLC-ESI-IT-TOF/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 959:49-54. [PMID: 24747524 DOI: 10.1016/j.jchromb.2014.03.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 10/25/2022]
Abstract
4-Methylpiperazine-1-carbodithiocacid-3-cyano-3,3-diphenylpropyl ester hydrochloride (TM208) was a potential antitumor new drug with many preliminary studies in pharmacokinetics and pharmacodynamics. This study aims to determine whether TM208 elicits toxic effects by metabonomics for the first time. Sprague Dawley (SD) rats were exposured to TM208 at a single therapeutic dose (100mg/kg/d) for 5 days, metabolites of urine samples from both control and TM208-treated groups were analyzed using high performance liquid chromatography-electrospray ionization source in combination with hybrid ion trap and high-resolution time-of-flight mass spectrometry (HPLC-ESI-IT-TOF/MS). Metabolites such as aminoadipic acid, creatine, gluconic acid, cis-aconitic acid, succinic acid and pipecolic acid which changed significantly, were identified as potential biomarkers. These results suggest that the changes in urinary metabolites of rats after exposure to TM208 were mainly related to energy metabolism and amino acid metabolism, which may be helpful to further understand the mechanism of TM208 toxicity in rats and a new drug development.
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Affiliation(s)
- Haisong Yang
- State Key Laboratory of Natural and Biomimetic and Drugs and Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences and Peking University, Beijing 100191, PR China
| | - Wensi Lin
- State Key Laboratory of Natural and Biomimetic and Drugs and Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences and Peking University, Beijing 100191, PR China
| | - Jianmei Zhang
- State Key Laboratory of Natural and Biomimetic and Drugs and Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences and Peking University, Beijing 100191, PR China
| | - Weiwei Lin
- State Key Laboratory of Natural and Biomimetic and Drugs and Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences and Peking University, Beijing 100191, PR China
| | - Peng Xu
- State Key Laboratory of Natural and Biomimetic and Drugs and Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences and Peking University, Beijing 100191, PR China
| | - Jing Li
- State Key Laboratory of Natural and Biomimetic and Drugs and Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences and Peking University, Beijing 100191, PR China
| | - Xiaomei Ling
- State Key Laboratory of Natural and Biomimetic and Drugs and Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences and Peking University, Beijing 100191, PR China.
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69
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Murphy JP, Everley RA, Coloff JL, Gygi SP. Combining amine metabolomics and quantitative proteomics of cancer cells using derivatization with isobaric tags. Anal Chem 2014; 86:3585-93. [PMID: 24611633 PMCID: PMC3983006 DOI: 10.1021/ac500153a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
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Quantitative metabolomics and proteomics
technologies are powerful
approaches to explore cellular metabolic regulation. Unfortunately,
combining the two technologies typically requires different LC-MS
setups for sensitive measurement of metabolites and peptides. One
approach to enhance the analysis of certain classes of metabolites
is by derivatization with various types of tags to increase ionization
and chromatographic efficiency. We demonstrate here that derivatization
of amine metabolites with tandem mass tags (TMT), typically used in
multiplexed peptide quantitation, facilitates amino acid analysis
by standard nanoflow reversed-phase LC-MS setups used for proteomics.
We demonstrate that this approach offers the potential to perform
experiments at the MS1-level using duplex tags or at the MS2-level
using novel 10-plex reporter ion-containing isobaric tags for multiplexed
amine metabolite analysis. We also demonstrate absolute quantitative
measurements of amino acids conducted in parallel with multiplexed
quantitative proteomics, using similar LC-MS setups to explore cellular
amino acid regulation. We further show that the approach can also
be used to determine intracellular metabolic labeling of amino acids
from glucose carbons.
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Affiliation(s)
- J Patrick Murphy
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
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70
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Zheng XF, Tian JS, Liu P, Xing J, Qin XM. Analysis of the restorative effect of Bu-zhong-yi-qi-tang in the spleen-qi deficiency rat model using (1)H-NMR-based metabonomics. JOURNAL OF ETHNOPHARMACOLOGY 2014; 151:912-920. [PMID: 24333365 DOI: 10.1016/j.jep.2013.12.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/23/2013] [Accepted: 12/01/2013] [Indexed: 06/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Bu-zhong-yi-qi-tang (BT) is a classical formula for the treatment of spleen-qi descending, visceroptosis with hyposplenic qi, uterine prolapse, and rectal prolapse due to chronic diarrhea in traditional Chinese medicine (TCM) and has been identified as an effective drug for the treatment of TCM spleen-qi deficiency in clinical practice. The present study aimed to investigate the restorative effect and the potential mechanisms of Bu-zhong-yi-qi-tang in a rat spleen-qi deficiency model using (1)H-NMR-based metabonomics. MATERIALS AND METHODS The rat spleen-qi deficiency model was established as follows: oral administration of Radix Rhei extract (equivalent to 10g/kg body weight of the crude drug), loaded swimming, and starvation for 24h. Each of these treatments was administered consecutively every three days. Sixty male SD rats were randomly divided into five groups, and three of the groups received a different oral dose of the aqueous extract of Bu-zhong-yi-qi-tang during the last seven days of the three-week experimental period. The body weight and motor behavior of the rats were measured and recorded once a week. The endogenous metabolites in the plasma were analyzed using NMR in conjunction with multivariate and statistical techniques. In addition, the liver and spleen were removed and weighed. RESULTS All of the rats in the spleen-qi deficiency group presented pasty loose stools, inactiveness, grouping, a decrease in swimming endurance, and lackluster, loose, and disorderly behavior in addition to a significant decrease in body weight, spleen weight, and liver weight. In contrast, the abovementioned demonstrations were reversed to a certain extent in the rats treated with Bu-zhong-yi-qi-tang compared with the model group (p<0.05, p<0.01). A significant separation was determined between the control and model groups in the PCA score plot, which indicates that the spleen-qi deficiency model was successfully duplicated. The changes in the levels of endogenous metabolites in the plasma included lower levels of valine, leucine, and O-acetyl-glycoprotein and a higher concentration of lactate in the spleen-qi deficiency group compared with the control group. Treatment with Bu-zhong-yi-qi-tang at least partially returned the levels of these metabolites to the normal levels. CONCLUSIONS The restorative effects of Bu-zhong-yi-qi-tang in rats with spleen-qi deficiency were confirmed, and four endogenous metabolites were identified as potential biomarkers of the symptoms of spleen-qi deficiency and most likely play roles in the changes observed in certain metabolic pathways, such as the energy, protein, and glycolytic metabolisms.
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Affiliation(s)
- Xiao-Fen Zheng
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, PR China
| | - Jun-Sheng Tian
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, PR China.
| | - Peng Liu
- Shanxi Pharmaceutical College, Taiyuan 030031, PR China
| | - Jie Xing
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, PR China
| | - Xue-Mei Qin
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, PR China
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71
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Ramsubramaniam N, Tao F, Li S, Marten MR. Novel and cost-effective 6-plex isobaric tagging reagent, DiART, is effective for identification and relative quantification of complex protein mixtures using PQD fragmentation. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1032-1041. [PMID: 24078244 DOI: 10.1002/jms.3249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 05/30/2013] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Deuterium isobaric Amine Reactive Tag (DiART) reagents facilitate relative quantification during proteomic analysis in a functionally similar manner to commercially available isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass tag (TMT) reagents. In contrast to iTRAQ and TMT, DiART reagents incorporate deuterium isotopes which significantly reduce the number of required synthesis steps and hence have potential to significantly reduce reagent production cost. We examined the capability of DiART for performing quantitative proteomic experiments using a linear ion-trap mass spectrometer with Pulsed Q Dissociation (PQD) fragmentation. Using a synthetic peptide tagged with DiART reagent, we observed a precise mass shift of 144.79 Da on the triply charged precursor ion, which shows complete derivatization of the N-terminus and ε-amino group of lysine. A DiART tagged tryptic digest of bovine serum albumin showed a sequence coverage of 57.99% which was very comparable to that showed by iTRAQ, 54.77%. Furthermore, a ten protein mixture tagged with DiART reagents and mixed in 1:1:1:1:1:1 exhibited < 15% error, whereas a linear trend (slope of 1.085) was observed when tagged proteins were mixed in the ratio 2:1:2:4:10:14 and plotted against theoretical ratios. Finally, when complex cell-wall protein mixtures from the model fungus A. nidulans were tagged with DiART reagents and mixed in different ratios, they exhibited similar trends. We conclude that DiART reagents are capable of performing quantitative proteomic experiments using PQD on a linear ion trap mass spectrometer.
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Affiliation(s)
- Nikhil Ramsubramaniam
- Department of Chemical, Biochemical and Environmental Engineering, UMBC, Engineering Building, Rm 314, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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72
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Relative quantification of biomarkers using mixed-isotope labeling coupled with MS. Bioanalysis 2013; 4:2525-41. [PMID: 23157360 DOI: 10.4155/bio.12.208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The identification and quantification of important biomarkers is a critical first step in the elucidation of biological systems. Biomarkers take many forms as cellular responses to stimuli and can be manifested during transcription, translation, and/or metabolic processing. Increasingly, researchers have relied upon mixed-isotope labeling (MIL) coupled with MS to perform relative quantification of biomarkers between two or more biological samples. MIL effectively tags biomarkers of interest for ease of identification and quantification within the mass spectrometer by using isotopic labels that introduce a heavy and light form of the tag. In addition to MIL coupled with MS, a number of other approaches have been used to quantify biomarkers including protein gel staining, enzymatic labeling, metabolic labeling, and several label-free approaches that generate quantitative data from the MS signal response. This review focuses on MIL techniques coupled with MS for the quantification of protein and small-molecule biomarkers.
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73
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Metabolic signatures of esophageal cancer: NMR-based metabolomics and UHPLC-based focused metabolomics of blood serum. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1207-16. [PMID: 23524237 DOI: 10.1016/j.bbadis.2013.03.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 01/28/2013] [Accepted: 03/10/2013] [Indexed: 12/14/2022]
Abstract
Focused metabolic profiling is a powerful tool for the determination of biomarkers. Here, a more global proton nuclear magnetic resonance ((1)H NMR)-based metabolomic approach coupled with a relative simple ultra high performance liquid chromatography (UHPLC)-based focused metabolomic approach was developed and compared to characterize the systemic metabolic disturbances underlying esophageal cancer (EC) and identify possible early biomarkers for clinical prognosis. Serum metabolic profiling of patients with EC (n=25) and healthy controls (n=25) was performed by using both (1)H NMR and UHPLC, and metabolite identification was achieved by multivariate statistical analysis. Using orthogonal projection to least squares discriminant analysis (OPLS-DA), we could distinguish EC patients from healthy controls. The predictive power of the model derived from the UHPLC-based focused metabolomics performed better in both sensitivity and specificity than the results from the NMR-based metabolomics, suggesting that the focused metabolomic technique may be of advantage in the future for the determination of biomarkers. Moreover, focused metabolic profiling is highly simple, accurate and specific, and should prove equally valuable in metabolomic research applications. A total of nineteen significantly altered metabolites were identified as the potential disease associated biomarkers. Significant changes in lipid metabolism, amino acid metabolism, glycolysis, ketogenesis, tricarboxylic acid (TCA) cycle and energy metabolism were observed in EC patients compared with the healthy controls. These results demonstrated that metabolic profiling of serum could be useful as a screening tool for early EC diagnosis and prognosis, and might enhance our understanding of the mechanisms involved in the tumor progression.
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74
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Lv H. Mass spectrometry-based metabolomics towards understanding of gene functions with a diversity of biological contexts. MASS SPECTROMETRY REVIEWS 2013; 32:118-128. [PMID: 22890819 DOI: 10.1002/mas.21354] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 01/25/2012] [Accepted: 03/30/2012] [Indexed: 06/01/2023]
Abstract
Currently, mass spectrometry-based metabolomics studies extend beyond conventional chemical categorization and metabolic phenotype analysis to understanding gene function in various biological contexts (e.g., mammalian, plant, and microbial). These novel utilities have led to many innovative discoveries in the following areas: disease pathogenesis, therapeutic pathway or target identification, the biochemistry of animal and plant physiological and pathological activities in response to diverse stimuli, and molecular signatures of host-pathogen interactions during microbial infection. In this review, we critically evaluate the representative applications of mass spectrometry-based metabolomics to better understand gene function in diverse biological contexts, with special emphasis on working principles, study protocols, and possible future development of this technique. Collectively, this review raises awareness within the biomedical community of the scientific value and applicability of mass spectrometry-based metabolomics strategies to better understand gene function, thus advancing this application's utility in a broad range of biological fields.
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Affiliation(s)
- Haitao Lv
- Center for Women's Infectious Diseases Research, Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
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75
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Shi B, Tian J, Xiang H, Guo X, Zhang L, Du G, Qin X. A 1H-NMR plasma metabonomic study of acute and chronic stress models of depression in rats. Behav Brain Res 2013; 241:86-91. [DOI: 10.1016/j.bbr.2012.11.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/20/2012] [Accepted: 11/24/2012] [Indexed: 11/26/2022]
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76
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Yuan W, Edwards JL, Li S. Global profiling of carbonyl metabolites with a photo-cleavable isobaric labeling affinity tag. Chem Commun (Camb) 2013; 49:11080-2. [DOI: 10.1039/c3cc45956j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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77
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Bharadwaj AS, Appukuttan B, Wilmarth PA, Pan Y, Stempel AJ, Chipps TJ, Benedetti EE, Zamora DO, Choi D, David LL, Smith JR. Role of the retinal vascular endothelial cell in ocular disease. Prog Retin Eye Res 2013; 32:102-80. [PMID: 22982179 PMCID: PMC3679193 DOI: 10.1016/j.preteyeres.2012.08.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 12/14/2022]
Abstract
Retinal endothelial cells line the arborizing microvasculature that supplies and drains the neural retina. The anatomical and physiological characteristics of these endothelial cells are consistent with nutritional requirements and protection of a tissue critical to vision. On the one hand, the endothelium must ensure the supply of oxygen and other nutrients to the metabolically active retina, and allow access to circulating cells that maintain the vasculature or survey the retina for the presence of potential pathogens. On the other hand, the endothelium contributes to the blood-retinal barrier that protects the retina by excluding circulating molecular toxins, microorganisms, and pro-inflammatory leukocytes. Features required to fulfill these functions may also predispose to disease processes, such as retinal vascular leakage and neovascularization, and trafficking of microbes and inflammatory cells. Thus, the retinal endothelial cell is a key participant in retinal ischemic vasculopathies that include diabetic retinopathy and retinopathy of prematurity, and retinal inflammation or infection, as occurs in posterior uveitis. Using gene expression and proteomic profiling, it has been possible to explore the molecular phenotype of the human retinal endothelial cell and contribute to understanding of the pathogenesis of these diseases. In addition to providing support for the involvement of well-characterized endothelial molecules, profiling has the power to identify new players in retinal pathologies. Findings may have implications for the design of new biological therapies. Additional progress in this field is anticipated as other technologies, including epigenetic profiling methods, whole transcriptome shotgun sequencing, and metabolomics, are used to study the human retinal endothelial cell.
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Affiliation(s)
| | | | - Phillip A. Wilmarth
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University
| | - Yuzhen Pan
- Casey Eye Institute, Oregon Health & Science University
| | | | | | | | | | - Dongseok Choi
- Department of Public Health and Preventive Medicine, Oregon Health & Science University
| | - Larry L. David
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University
| | - Justine R. Smith
- Casey Eye Institute, Oregon Health & Science University
- Department of Cell & Developmental Biology, Oregon Health & Science University
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78
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Separation technique for the determination of highly polar metabolites in biological samples. Metabolites 2012; 2:496-515. [PMID: 24957644 PMCID: PMC3901216 DOI: 10.3390/metabo2030496] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 11/23/2022] Open
Abstract
Metabolomics is a new approach that is based on the systematic study of the full complement of metabolites in a biological sample. Metabolomics has the potential to fundamentally change clinical chemistry and, by extension, the fields of nutrition, toxicology, and medicine. However, it can be difficult to separate highly polar compounds. Mass spectrometry (MS), in combination with capillary electrophoresis (CE), gas chromatography (GC), or high performance liquid chromatography (HPLC) is the key analytical technique on which emerging "omics" technologies, namely, proteomics, metabolomics, and lipidomics, are based. In this review, we introduce various methods for the separation of highly polar metabolites.
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79
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Chen Z, Wang Q, Lin L, Tang Q, Edwards JL, Li S, Liu S. Comparative evaluation of two isobaric labeling tags, DiART and iTRAQ. Anal Chem 2012; 84:2908-15. [PMID: 22404494 DOI: 10.1021/ac203467q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Isobaric tags have broad applications in both basic and translational research, as demonstrated by the widely used isobaric tag for relative and absolute quantitation (iTRAQ). Recent results from large-scale quantitative proteomics projects, however, indicate that protein quantification by iTRAQ is often biased in complex biological samples. Here, we report the application of another isobaric tag, deuterium isobaric amine reactive tag (DiART), for quantifying the proteome of Thermoanaerobacter tengcongensis (T. tengcongensis), a thermophilic bacterium first discovered in China. We compared the performance of DiART with iTRAQ from several different aspects, including their fragmentation mechanisms, the number of identified proteins, and the accuracy of quantification. Our results revealed that, as compared with iTRAQ, DiART yielded significantly stronger reporter ions, which did not reduce the number of identifiable peptides, but improved the signal-to-noise ratio (S/N) for quantification. Remarkably, we found that, under identical chromatography and mass spectrometry (MS) conditions, DiART exhibited less reporter ions ratio compression than iTRAQ, probably due to more reporter ions with higher intensities produced by DiART labeling. Taken together, we demonstrate that DiART is a valuable alternative of iTRAQ with enhanced performance for quantitative proteomics.
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Affiliation(s)
- Zhen Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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80
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Yuan W, Anderson KW, Li S, Edwards JL. Subsecond Absolute Quantitation of Amine Metabolites Using Isobaric Tags for Discovery of Pathway Activation in Mammalian Cells. Anal Chem 2012; 84:2892-9. [DOI: 10.1021/ac203453t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Wei Yuan
- Institute for Bioscience
and
Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| | - Kyle W. Anderson
- Institute for Bioscience
and
Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| | - Shuwei Li
- Institute for Bioscience
and
Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| | - James L. Edwards
- Institute for Bioscience
and
Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
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