Metabolomics Insights Into Pathophysiological Mechanisms of Interstitial Cystitis

Oliver Fiehn,김자영 대한배뇨장애요실금학회 2014 International Neurourology Journal Vol.18 No.3

Interstitial cystitis (IC), also known as painful bladder syndrome or bladder pain syndrome, is a chronic lower urinary tract syndrome characterized by pelvic pain, urinary urgency, and increased urinary frequency in the absence of bacterial infection or identifiable clinicopathology. IC can lead to long-term adverse effects on the patient’s quality of life. Therefore, early diagnosis and better understanding of the mechanisms underlying IC are needed. Metabolomic studies of biofluids have become a powerful method for assessing disease mechanisms and biomarker discovery, which potentially address these important clinical needs. However, limited intensive metabolic profiles have been elucidated in IC. The article is a short review on metabolomic analyses that provide a unique fingerprint of IC with a focus on its use in determining a potential diagnostic biomarker associated with symptoms, a response predictor of therapy, and a prognostic marker.

Metabolomic Response of Chlamydomonas reinhardtii to the Inhibition of Target of Rapamycin (TOR) by Rapamycin

( Do Yup Lee ),( Oliver Fiehn ) 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.7

Rapamycin, known as an inhibitor of Target of Rapamycin (TOR), is an immunosuppressant drug used to prevent rejection in organ transplantation. Despite the close association of the TOR signaling cascade with various scopes of metabolism, it has not yet been thoroughly investigated at the metabolome level. In our current study, we applied mass spectrometric analysis for profiling primary metabolism in order to capture the responsive dynamics of the Chlamydomonas metabolome to the inhibition of TOR by rapamycin. Accordingly, we identified the impact of the rapamycin treatment at the level of metabolomic phenotypes that were clearly distinguished by multivariate statistical analysis. Pathway analysis pinpointed that inactivation of the TCA cycle was accompanied by the inhibition of cellular growth. Relative to the constant suppression of the TCA cycle, most amino acids were significantly increased in a time-dependent manner by longer exposure to rapamycin treatment, after an initial down-regulation at the early stage of exposure. Finally, we explored the isolation of the responsive metabolic factors into the rapamycin treatment and the culture duration, respectively.

Systems biology: mass-spectrometry based functional metabolomics and integrative analysis with proteome research

Do Yup Lee,Oliver Fiehn 한국생물공학회 2013 한국생물공학회 학술대회 Vol.2013 No.4

Metabolomics-driven systems biology of microalga, Chlamydomonas reinhardtii.

Do Yup LEE,Oliver FIEHN 한국생물공학회 2013 한국생물공학회 학술대회 Vol.2013 No.10

Profiling of Disease-Related Metabolites in Grapevine Internode Tissues Infected with Agrobacterium vitis

정성민,허윤영,John E. Preece,Oliver Fiehn,김영호 한국식물병리학회 2016 Plant Pathology Journal Vol.32 No.6

Green shoot cuttings of 10 different grapevine specieswere inoculated with Agrobacterium vitis to finddisease-related metabolites in the grapevine. Crowngalls formed 60 days after inoculation varied in gallseverity (GS) evaluated by gall incidence (GI) andgall diameter (GD), which were classified into threeresponse types as RR (low GI and small GD), SR (highGI and small GD), and SS (high GI and large GD),corresponding to resistant, moderately resistant, andsusceptible responses, respectively. In this, 4, 4, and 2Vitis species were classified into RR, SR, and SS, respectively. Gas chromatography mass spectrometry(GC-MS) analysis of the grapevine stem metaboliteswith A. vitis infection showed 134 metabolites in variouscompound classes critically occurred, which weredifferentially clustered with the response types by theprincipal component analysis. Multivariate analysis ofthe metabolite profile revealed that 11 metabolites increasedsignificantly in relation to the response types,mostly at post-inoculation stages, more prevalently (8metabolites) at two days after inoculation than otherstages, and more related to SS (7 metabolites) than RR(3 metabolites) or SR (one metabolite). This suggestsmost of the disease-related metabolites may be rarelypre-existing but mostly induced by pathogen infectionlargely for facilitating gall development except stilbenecompound resveratrol, a phytoalexin that may be involvedin the resistance response. All of these aspectsmay be used for the selection of resistant grapevinecultivars and their rootstocks for the control of thecrown gall disease of the grapevine.

Profiling of Disease-Related Metabolites in Grapevine Internode Tissues Infected with Agrobacterium vitis

Jung, Sung-Min,Hur, Youn-Young,Preece, John E.,Fiehn, Oliver,Kim, Young-Ho The Korean Society of Plant Pathology 2016 Plant Pathology Journal Vol.32 No.6

Green shoot cuttings of 10 different grapevine species were inoculated with Agrobacterium vitis to find disease-related metabolites in the grapevine. Crown galls formed 60 days after inoculation varied in gall severity (GS) evaluated by gall incidence (GI) and gall diameter (GD), which were classified into three response types as RR (low GI and small GD), SR (high GI and small GD), and SS (high GI and large GD), corresponding to resistant, moderately resistant, and susceptible responses, respectively. In this, 4, 4, and 2 Vitis species were classified into RR, SR, and SS, respectively. Gas chromatography mass spectrometry (GC-MS) analysis of the grapevine stem metabolites with A. vitis infection showed 134 metabolites in various compound classes critically occurred, which were differentially clustered with the response types by the principal component analysis. Multivariate analysis of the metabolite profile revealed that 11 metabolites increased significantly in relation to the response types, mostly at post-inoculation stages, more prevalently (8 metabolites) at two days after inoculation than other stages, and more related to SS (7 metabolites) than RR (3 metabolites) or SR (one metabolite). This suggests most of the disease-related metabolites may be rarely pre-existing but mostly induced by pathogen infection largely for facilitating gall development except stilbene compound resveratrol, a phytoalexin that may be involved in the resistance response. All of these aspects may be used for the selection of resistant grapevine cultivars and their rootstocks for the control of the crown gall disease of the grapevine.

Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network

Kim, Taehyong,Dreher, Kate,Nilo-Poyanco, Ricardo,Lee, Insuk,Fiehn, Oliver,Lange, Bernd Markus,Nikolau, Basil J.,Sumner, Lloyd,Welti, Ruth,Wurtele, Eve S.,Rhee, Seung Y. American Society of Plant Biologists 2015 Plant Physiology Vol.167 No.4

<P><I>Global patterns of metabolic responses upon single gene perturbations are specific to gene functions, but they are coordinated with characteristics of the perturbed genes.</I></P><P>Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (<I>Arabidopsis thaliana</I>) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.</P>

Evaluation and Optimization of Metabolome Sample Preparation Methods for Saccharomyces cerevisiae

Kim, Sooah,Lee, Do Yup,Wohlgemuth, Gert,Park, Hyong Seok,Fiehn, Oliver,Kim, Kyoung Heon American Chemical Society 2013 ANALYTICAL CHEMISTRY - Vol.85 No.4

<P>Metabolome sampling is one of the most important factors that determine the quality of metabolomics data. The main steps in metabolite sample preparation include quenching and metabolite extraction. Quenching with 60% (v/v) cold methanol at −40 °C has been most commonly used for Saccharomyces cerevisiae, and this method was recently modified as “leakage-free cold methanol quenching” using pure methanol at −40 °C. Boiling ethanol (75%, v/v) and cold pure methanol are the most widely used extraction solvents for S. cerevisiae. In the present study, metabolome sampling protocols, including the above methods, were evaluated by analyzing 110 identified intracellular metabolites of S. cerevisiae using gas chromatography/time-of-flight mass spectrometry. According to our results, fast filtration followed by washing with an appropriate volume of water can minimize the metabolite loss due to cell leakage as well as the contamination by extracellular metabolites. For metabolite extraction, acetonitrile/water mixture (1:1, v/v) at −20 °C was the most effective. These results imply that the systematic evaluation of existing methods and the development of customized methods for each microorganism are critical for metabolome sample preparation to facilitate the reliable and accurate analysis of metabolome.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancham/2013/ancham.2013.85.issue-4/ac302881e/production/images/medium/ac-2012-02881e_0005.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ac302881e'>ACS Electronic Supporting Info</A></P>

Determination of elemental compositions by gas chromatography/time-of-flight mass spectrometry using chemical and electron ionization

Abate, Salvatore,Ahn, Yun Gyong,Kind, Tobias,Cataldi, Tommaso R. I.,Fiehn, Oliver John Wiley Sons, Ltd. 2010 Rapid communications in mass spectrometry Vol.24 No.8

<P>Many metabolomic applications use gas chromatography/mass spectrometry (GC/MS) under standard 70 eV electron ionization (EI) parameters. However, the abundance of molecular ions is often extremely low, impeding the calculation of elemental compositions for the identification of unknown compounds. On changing the beam-steering voltage of the ion source, the relative abundances of molecular ions at 70 eV EI were increased up to ten-fold for alkanes, fatty acid methyl esters and trimethylsilylated metabolites, concomitant with 2-fold absolute increases in ion intensities. We have compared the abundance, mass accuracy and isotope ratio accuracy of molecular species in EI with those in chemical ionization (CI) with methane as reagent gas under high-mass tuning. Thirty-three peaks of a diverse set of trimethylsilylated metabolites were analyzed in triplicate, resulting in 342 ion species ([M+H]<SUP>+</SUP>, [M–CH<SUB>3</SUB>]<SUP>+</SUP> for CI and [M]<SUP>+.</SUP>, [M–CH<SUB>3</SUB>]<SUP>+.</SUP> for EI). On average, CI yielded 8-fold more intense molecular species than EI. Using internal recalibration, average mass errors of 1.8 ± 1.6 mm/z units and isotope ratio errors of 2.3 ± 2.0% (A+1/A ratio) and 1.7 ± 1.8% (A+2/A ratio) were obtained. When constraining lists of calculated elemental compositions by chemical and heuristic rules using the Seven Golden Rules algorithm and PubChem queries, the correct formula was retrieved as top hit in 60% of the cases and within the top-3 hits in 80% of the cases. Copyright © 2010 John Wiley & Sons, Ltd.</P>

Comparative evaluation of extraction methods for simultaneous mass-spectrometric analysis of complex lipids and primary metabolites from human blood plasma

Lee, Do Yup,Kind, Tobias,Yoon, Young-Ran,Fiehn, Oliver,Liu, Kwang-Hyeon Springer-Verlag 2014 Analytical and Bioanalytical Chemistry Vol.406 No.28