Description of HMGU - Helmholtz Zentrum München
Description of HMGU - Helmholtz Zentrum München
Description of HMGU - Helmholtz Zentrum München
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Metabolomic Platform at <strong>HMGU</strong><br />
metaP<br />
Jerzy Adamski<br />
<strong>Helmholtz</strong> <strong>Zentrum</strong> <strong>München</strong> (<strong>HMGU</strong>)<br />
German Research Center for Environmental Health<br />
Institute <strong>of</strong> Experimental Genetics<br />
Genome Analysis Center<br />
Metabolomic Platform (metaP)<br />
Ingolstaedter Landstrasse 1<br />
D-85764 Neuherberg<br />
Germany<br />
Voice: +49-89-3187-3155 (Pr<strong>of</strong>. Jerzy Adamski, Head)<br />
Head)<br />
+49-89-3187-3231 (Dr. Cornelia Prehn, Metabolic Laboratory<br />
+49-89-3187-3722 (Julia Henrichs, Team assistance)<br />
Fax: +49-89-3187-3225<br />
Email: Adamski@helmholtz-muenchen.de<br />
Julia.Henrichs@helmholtz-muenchen.de<br />
Prehn@helmholtz-muenchen.de<br />
URL: http://www.helmholtz-muenchen.de/gac-metabolomics<br />
Contents<br />
<strong>Description</strong> <strong>of</strong> <strong>HMGU</strong> ............................................................... 2<br />
Portfolio................................................................................. 4<br />
Methods ................................................................................ 4<br />
SOP Example for human plasma samples ........................... 5<br />
Relevant Publications............................................................... 6<br />
Annex A................................................................................. 8<br />
Abbreviations used for metabolites .......................................... 13<br />
1
<strong>Description</strong> <strong>of</strong> <strong>HMGU</strong><br />
The <strong>Helmholtz</strong> <strong>Zentrum</strong> <strong>München</strong>, National Research Center for<br />
Environmental Health (<strong>HMGU</strong>), is a federally funded research center<br />
located in Neuherberg/Munich, Germany. Multidisciplinary research<br />
<strong>of</strong> the <strong>HMGU</strong> is focused on activities related to the protection <strong>of</strong><br />
man and his environment as well as the utilisation <strong>of</strong> scientific and<br />
technical knowledge to improve health care.<br />
Genome Analysis Center and Institute for Bioinformatics and<br />
Systems Biology (IBIS) jointly support participating laboratory<br />
(metaP, for Metabolomic Platform). It comprises experts in the<br />
biochemical, analytical and bioinformatics fields. The targeted<br />
quantitative metabomic pr<strong>of</strong>iling (FDA-validated kit) is based on the<br />
pioneering work by BIOCRATES Life Sciences (www.biocrates.at).<br />
We are equipped with state-<strong>of</strong>-the-art liquid handling and extraction<br />
robotics (Hamilton Microlab Star) and a high performance mass<br />
spectrometry instruments (API 4000 Q-Trap). Access to versatile<br />
post-equipment data processing is implemented.<br />
Pr<strong>of</strong>essor Jerzy Adamski (Adamski@helmholtz-muenchen.de) is<br />
Head <strong>of</strong> Genome Analysis Center (GAC) and the Metabolomic<br />
Plattform (MetaP). The GAC promotes high throughput research in<br />
genomic, metabolomic and proteomic mechanisms <strong>of</strong> the<br />
development and progression <strong>of</strong> complex diseases in man. Several<br />
human multifactorial diseases are associated with abnormal<br />
metabolism <strong>of</strong> sterols, lipids and fatty acids. Dr. Adamskis interests<br />
are to identify the factors, both at the genomic and metabolic<br />
levels, responsible for the pathogenesis <strong>of</strong> diseases. The strategy is<br />
based on translational approaches that bridge basic research with<br />
clinical application. He participates in the EU-project PROPATH.<br />
2
Associate Pr<strong>of</strong>essor Thomas Illig (illig@helmholtz-muenchen.de) is<br />
Head <strong>of</strong> the group “Molecular Epidemiology” <strong>of</strong> the <strong>HMGU</strong>. He has a<br />
longstanding experience in molecular and genetic epidemiology. He<br />
is in the advisory board <strong>of</strong> the federal government for metabolic<br />
diseases. Dr. Illig co-organised large population based and disease<br />
related epidemiological studies (e.g. KORA). One main focus is the<br />
analysis <strong>of</strong> cardiovascular diseases as well as <strong>of</strong> diabetes. Dr. Illig is<br />
principle investigator <strong>of</strong> subprojects in the German National<br />
Genome Research Net. He participates in EU-projects GABRIEL and<br />
NUTRIMENTHE.<br />
Associate Pr<strong>of</strong>essor Philippe Schmitt-Kopplin (schmitt-<br />
kopplin@helmholtz-muenchen.de) is group leader with a research<br />
focus on capillary separation techniques (CE, GC, LC) coupled to<br />
mass spectrometry, Fourier transform ion cyclotron mass<br />
spectrometry (FT/ICR-MS), multidimensional magnetic resonance<br />
spectroscopy (NMR), all applied in metabolomic studies. His<br />
research efforts are focused on the development <strong>of</strong> new and<br />
powerful research tools enabling the targeted and non targeted<br />
analysis <strong>of</strong> complex mixtures.<br />
Pr<strong>of</strong>essor Karsten Suhre (karsten.suhre@helmholtz-muenchen.de)<br />
is Pr<strong>of</strong>essor for Bioinformatics at the Ludwig-Maximilians-University<br />
and Head <strong>of</strong> the Department for Systematic Genome Analysis within<br />
the Institute for Bioinformatics and System Biology (IBIS) at <strong>HMGU</strong>.<br />
His personal interest is in genetically determined human<br />
metabotypes and their link to complex disease. Metabolomic studies<br />
in animal models, such as mice and bovine are used in complement<br />
to studies in a human population. He recently established MassTRIX<br />
service (http://masstrix.org) identifying chemical compounds from<br />
mass spectrometry analyses in their genomic context on KEGG<br />
pathway maps.<br />
3
Portfolio<br />
Targeted analysis <strong>of</strong> metabolites with high throughput quantitative<br />
mass spectrometry is a new and versatile tool for comprehensive<br />
phenotype analyses <strong>of</strong> large populations. MetaP platform is<br />
designed to extensively characterize metabolic pathways affected in<br />
early-onset and late development disease. The classes <strong>of</strong> analytes<br />
include (but are not limited to) lipids, sugars, and amino acids. We<br />
quantify 163 different metabolites in human serum and animal<br />
tissue samples (metabolites are described in Annex A). The analytes<br />
give clues both to identity and cross-talk <strong>of</strong> affected pathways in<br />
early forms <strong>of</strong> diseases. Several complementary approaches are<br />
possible: (i) bridge the gap between phenotypic observations and<br />
clinical outcome by metabolomics data (ii) characterisation <strong>of</strong> the<br />
metabolic states in tissue samples from human and animal models.<br />
Methods<br />
All sample processing should follow SOP as provided from <strong>HMGU</strong><br />
(see example below). Tissues and body fluids should be portioned<br />
and snap-frozen as soon as possible after collection.<br />
Human or animal plasma (50µL) or tissue (100mg) is requested for<br />
a single assay. Samples will be processed in a fully automated<br />
manner in multiwell plates using Hamilton robotics station.<br />
Metabolite spectrum is designed to monitor the metabolism <strong>of</strong><br />
sugars, acylcarnitines, amino acids, glycerophospholipids and<br />
sphingolipids. The resulting dataset will be subject to several levels<br />
<strong>of</strong> data analyses, starting with metabolite identification and<br />
quantification based on the raw multiplexed MS/MS spectra and the<br />
knowledge <strong>of</strong> the spiked isotope reference markers. In this step,<br />
BIOCRATES Life Sciences MarkerIDQ s<strong>of</strong>tware shall be used as<br />
provided with the AbsoluteIDQ kit.<br />
4
In a second step, correlations within the metabolite dataset could<br />
be combined with external biochemical knowledge (e.g. from<br />
metabolic pathway maps, KEGG), using bioinformatics tools<br />
developed specifically for every project at <strong>HMGU</strong>-IBIS.<br />
Throughput is at present stable at 160 samples a day.<br />
SOP Example for human plasma samples<br />
(Please request the SOP for mouse plasma or other matrices)<br />
Collection and handling <strong>of</strong> plasma for metabolomics<br />
The AbsoluteIDQ kit has been designed for performing targeted<br />
metabolomics using plasma samples. To assure high quality results<br />
some guidelines, which are described in this section, need to be<br />
followed.<br />
Blood samples are directly collected into tubes that contain<br />
anticoagulants. The preferred anticoagulant is EDTA but also<br />
heparin is acceptable. It is not recommended to use citrate!<br />
Alternatively, blood can be drawn with a plastic syringe and is<br />
subsequently transferred into an EDTA coated tube.<br />
Immediately, the samples need to be stored on ice until<br />
centrifugation. Centrifugation should take place as soon as possible.<br />
Suitable spinning conditions would be 10 min at 2000 x g at 4°C.<br />
The resulting plasma is transferred into fresh tubes without carry-<br />
over <strong>of</strong> any blood cells. Plasma samples need to be frozen in small<br />
portions (200-300 microliters) immediately and stored at -80°C<br />
until further use with the kit.<br />
5
Relevant Publications<br />
Prehn, C., Ströhle, F., Haller, F., Keller, B., Hrabě de Angelis, M.,<br />
Adamski, J. and Mindnich, R. (2007) A Comparison Of Methods For<br />
Assays Of Steroidogenic Enzymes: New GC/MS Versus HPLC And<br />
TLC. Purdue University Press, West Lafayette, Indiana, USA.<br />
Guo, K., Lukacik, P., Papagrigoriou, E., Meier, M., Lee, W.H.,<br />
Adamski, J. and Oppermann, U. Characterization <strong>of</strong> Human DHRS6,<br />
an Orphan Short Chain Dehydrogenase/ Reductase Enzyme: a<br />
novel, cytosolic type 2 R-beta-hydroxybutyrate dehydrogenase. J<br />
Biol Chem, 281: 10291-10297 (2006)<br />
Herbert A, Gerry NP, McQueen MB, Heid IM, Pfeufer A, Illig T,<br />
Wichmann HE, Meitinger T, Hunter D, Hu FB, Colditz G, Hinney A,<br />
Hebebrand J, Koberwitz K, Zhu X, Cooper R, Ardlie K, Lyon H,<br />
Hirschhorn JN, Laird NM, Lenburg ME, Lange C, Christman MF.A<br />
common genetic variant 10 kb upstream <strong>of</strong> INSIG2 is associated<br />
with adult and childhood obesity. Science. 312: 279-283 (2006)<br />
Döring A, Gieger C, Mehta D, Gohlke H, Prokisch H, Coassin S,<br />
Fischer G, Henke K, Klopp N, Kronenberg F, Paulweber B, Pfeufer A,<br />
Rosskopf D, Völzke H, Illig T, Meitinger T, Wichmann HE, Meisinger<br />
C. SLC2A9 influences uric acid concentrations with pronounced sex-<br />
specific effects. Nat Genet. (2008) 2008 Apr;40(4):430-6.<br />
Chen, J., X. Zhao, R. Lehmann, J. Fritsche, P. Yin, Ph. Schmitt-<br />
Kopplin, W. Wang, X. Lu, H.U. Häring, E. D. Schleicher, G. Xu,<br />
Strategy for biomarker discovery and identification based on LC-<br />
MSn in metabonomics research. Anal. Chem. 80: 1280-89 (2008)<br />
6
Altmaier E, Ramsay SL, Graber A, Mewes HW, Weinberger KM,<br />
Suhre K.: Bioinformatics analysis <strong>of</strong> targeted metabolomics -<br />
uncovering old and new tales <strong>of</strong> diabetic mice under medication.<br />
Endocrinology (2008) 149(7):3478-89<br />
K. Suhre, P. Schmitt-Kopplin MassTRIX: Mass TRanslator Into<br />
Pathways, Nucleic Acid Research (2008) 2008 Jul 1;36 (Web Server<br />
issue):W481-4.<br />
Gieger, Ch., L. Geistlinger, E., M. Hrabé de Angelis, F. Kronenberg,<br />
Th. Meitinger, H.-W. Mewes, H.-E. Wichmann, K.M. Weinberger, J.<br />
Adamski, Illig, T., Suhre, K. Genetics meets metabolomics: a<br />
genome-wide association study <strong>of</strong> metabolite pr<strong>of</strong>iles in human<br />
serum. PLOS Genetics, 2008 in press<br />
7
Annex A:<br />
Metabolites assayed and limits <strong>of</strong> assays<br />
Acylcarnitines 1<br />
8
Acylcarnitines 2<br />
Amino Acids<br />
Sugars<br />
9
Glycerophospholipids 1<br />
10
Glycerophospholipids 2<br />
11
Glycerophospholipids 3<br />
Shingolipids<br />
12
Abbreviations used for metabolites<br />
sugars<br />
Hn for nhexose,<br />
dH for desoxyhexose<br />
UA for uronic acid<br />
HNAc for N-acetylglucosamine<br />
acylcarnitines (Cx:y, where x denotes the number <strong>of</strong> carbons in<br />
the side chain and y the number <strong>of</strong> double bonds)<br />
sphingomyelins (SMx:y)<br />
sphingomyelin derivatives, such as N-<br />
hydroxyldicarboacyloylsphingosyl-phosphocholine<br />
(SM(OH,COOH)x:y) and N- hydroxylacyloylsphingosylphosphocholine<br />
(SM (OH)x:y)<br />
Glycerophospholipids are further differentiated with respect to<br />
the presence <strong>of</strong> ester (a) and ether (e) bonds in the glycerol<br />
moiety, where two letters (aa, ea, or ee) denote that the first as<br />
well as the second position <strong>of</strong> the glycerol unit are bound to a fatty<br />
acid residue, while a single letter (a or e) indicates a bond with only<br />
one fatty acid residue.<br />
E.g. PC_ea_33:1 denotes a plasmalogen phosphatidylcholine with<br />
33 carbons in the two fatty acid side chains and a single double<br />
bond in one <strong>of</strong> them.<br />
glycero-phosphatidic acids (PA),<br />
glycero-phosphatidylcholines (PC),<br />
glycero-phosphatidylethanolamines (PE),<br />
phosphatidylglycerols (PG),<br />
glycero-phosphatidylinositols (PI)<br />
glycerophosphatidylinositol-bisphosphate (PIP2) and - triphosphate<br />
(PIP3)<br />
glycerophosphatidylserines (PS).<br />
13