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      Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study

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          Abstract

          Serum metabolite profiling in Duchenne muscular dystrophy (DMD) may enable discovery of valuable molecular markers for disease progression and treatment response. Serum samples from 51 DMD patients from a natural history study and 22 age-matched healthy volunteers were profiled using liquid chromatography coupled to mass spectrometry (LC-MS) for discovery of novel circulating serum metabolites associated with DMD. Fourteen metabolites were found significantly altered (1% false discovery rate) in their levels between DMD patients and healthy controls while adjusting for age and study site and allowing for an interaction between disease status and age. Increased metabolites included arginine, creatine and unknown compounds at m/z of 357 and 312 while decreased metabolites included creatinine, androgen derivatives and other unknown yet to be identified compounds. Furthermore, the creatine to creatinine ratio is significantly associated with disease progression in DMD patients. This ratio sharply increased with age in DMD patients while it decreased with age in healthy controls. Overall, this study yielded promising metabolic signatures that could prove useful to monitor DMD disease progression and response to therapies in the future.

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          Most cited references12

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          METLIN: a metabolite mass spectral database.

          Endogenous metabolites have gained increasing interest over the past 5 years largely for their implications in diagnostic and pharmaceutical biomarker discovery. METLIN (http://metlin.scripps.edu), a freely accessible web-based data repository, has been developed to assist in a broad array of metabolite research and to facilitate metabolite identification through mass analysis. METLINincludes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrometry (MS/MS) spectra, and LC/MS data.
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            CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets.

            Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottleneck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion modes, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. We demonstrate the utility of CAMERA in two different, easily adoptable plant metabolomics experiments, where the application of CAMERA drastically reduced the amount of manual analysis. © 2011 American Chemical Society
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              Is Open Access

              Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

              The causes and etiology of Crohn's disease (CD) are currently unknown although both host genetics and environmental factors play a role. Here we used non-targeted metabolic profiling to determine the contribution of metabolites produced by the gut microbiota towards disease status of the host. Ion Cyclotron Resonance Fourier Transform Mass Spectrometry (ICR-FT/MS) was used to discern the masses of thousands of metabolites in fecal samples collected from 17 identical twin pairs, including healthy individuals and those with CD. Pathways with differentiating metabolites included those involved in the metabolism and or synthesis of amino acids, fatty acids, bile acids and arachidonic acid. Several metabolites were positively or negatively correlated to the disease phenotype and to specific microbes previously characterized in the same samples. Our data reveal novel differentiating metabolites for CD that may provide diagnostic biomarkers and/or monitoring tools as well as insight into potential targets for disease therapy and prevention.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                15 April 2016
                2016
                : 11
                : 4
                : e0153461
                Affiliations
                [1 ]Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, United States of America
                [2 ]Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
                [3 ]Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC, United States of America
                [4 ]Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
                [5 ]Children’s National Medical Center and the George Washington University, Washington, DC, United States of America
                [6 ]Department of Physical Medicine and Rehabilitation, University of California Davis, School of Medicine, Davis, California, United States of America
                [7 ]Department of Pediatrics, University of Calgary, Alberta Children’s Hospital, Calgary, Alberta, Canada
                [8 ]Neurology Service, Department of Veteran Affairs Medical Center, Pittsburgh, Pennsylvania, United States of America
                [9 ]Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                Rutgers University -New Jersey Medical School, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: SMB AKC KG HS LPM EH CM JKM PRC EPH YH. Performed the experiments: AKC KG. Analyzed the data: SMB MN MH SR AKC YH SM. Wrote the paper: SMB MN MH SR AKC KG HS LPM EH CM JKM PRC EPH YH SM.

                Author information
                http://orcid.org/0000-0002-1400-3398
                Article
                PONE-D-15-45648
                10.1371/journal.pone.0153461
                4833348
                27082433
                4d511e15-8db5-4be9-8fb3-7c9968ad4d5b

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 2 November 2015
                : 30 March 2016
                Page count
                Figures: 5, Tables: 1, Pages: 18
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: P30CA051008
                Funded by: funder-id http://dx.doi.org/10.13039/100000069, National Institute of Arthritis and Musculoskeletal and Skin Diseases;
                Award ID: R01AR062380
                Funded by: funder-id http://dx.doi.org/10.13039/100000069, National Institute of Arthritis and Musculoskeletal and Skin Diseases;
                Award ID: P50AR060836
                The following grants contributed to the funding of this study: National Institutes of Health/National Cancer Institute grant P30CA051008 (for the Proteomics and Metabolomics shared resource), https://taggs.hhs.gov/AwardDetail.cfm?s_Award_Num=P30CA051008&n_Prog_Office_Code=110; National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases grant R01AR062380 (PI: CM, funded authors: SMB, HS, LPM, EH, CM, SM), https://taggs.hhs.gov/AwardDetail.cfm?s_Award_Num=R01AR062380&n_Prog_Office_Code=106; National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases grant P50AR060836 (PI: PRC, funded authors: PRC, EPH), https://taggs.hhs.gov/AwardDetail.cfm?s_Award_Num=P50AR060836&n_Prog_Office_Code=106.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Metabolism
                Metabolites
                Biology and Life Sciences
                Biochemistry
                Biomarkers
                Creatinine
                Physical Sciences
                Chemistry
                Chemical Compounds
                Organic Compounds
                Creatine
                Physical Sciences
                Chemistry
                Organic Chemistry
                Organic Compounds
                Creatine
                Physical Sciences
                Chemistry
                Chemical Compounds
                Salts
                Sulfates
                Medicine and Health Sciences
                Neurology
                Muscular Dystrophies
                Duchenne Muscular Dystrophy
                Medicine and Health Sciences
                Clinical Genetics
                X-Linked Traits
                Duchenne Muscular Dystrophy
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Linkage
                Sex Linkage
                X-Linked Traits
                Duchenne Muscular Dystrophy
                Biology and Life Sciences
                Biochemistry
                Biomarkers
                Medicine and Health Sciences
                Pharmacology
                Pharmacokinetics
                Drug Metabolism
                Biology and Life Sciences
                Biochemistry
                Hormones
                Androgens
                Testosterone
                Biology and Life Sciences
                Biochemistry
                Hormones
                Lipid Hormones
                Testosterone
                Custom metadata
                The fully processed data is available in the Supporting Information files. Raw data are available via the Dryad Digital Repository ( http://dx.doi.org/10.5061/dryad.qg6q2).

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