Karsten Suhre, PhD
Karsten Suhre, PhD
Professor of Physiology and Biophysics
Director of the Bioinformatics Core

PhD, Atmospheric Chemistry and Meteorology Modelling, University of Toulouse

Phone: (974) 4492 8482
Karsten Suhre

Bioinformatics Core
Virtual Metabolomics Core

Please consider submitting your next metabolomics paper to "Archives of Biochemistry and Biophysics" and request me as an editor in your cover letter.

 


Suhre Lab

Curriculum Vitae

09/2006 - 03/2011 Professor for Bioinformatics at the Ludwig-Maximilians-University (Faculty of Biology) in association with the Institute for Bioinformatics and Systems Biology (MIPS) at Helmholtz Zentrum München, Munich, Germany
(metabolomics)
10/2005 - 08/2006 Senior Scientist CNRS ("Directeur de Recherche") at Information Genomique & Structurale, Marseille, France
(bioinformatics and structural biology)
02/2002 - 09/2005 Scientist CNRS ("Charge de Recherche") at Information Genomique & Structurale, Marseille, France
(bioinformatics and structural biology)
26/10/2004 Habilitation bioinformatics and structural biology Université Aix-Marseille II, France [HDR thesis].
01/2000 - 01/2002 Project Engineer at Wilhelm Karmann GmbH, Osnabruck, Germany
(project management in the automobile industry, R&D department)
10/1994 - 12/1999 Scientist CNRS ("Charge de Recherche") CNRS at Laboratoire d'Aerologie, Toulouse, France
(atmospheric chemistry and meteorology modelling)
10/1993 - 09/1994 Postdoc at Laboratoire d'Aerologie (Marie-Curie fellowship)
(atmospheric chemistry and meteorology modelling)
01/1992 - 04/1994 Ph.D. Thesis at University of Toulouse, France 
(atmospheric chemistry and meteorology modelling)
10/1984 - 09/1991 Diplom Physik at University of Osnabruck, Germany 
(speciality of diploma thesis: quantum field theory) 

Vordiplom Mathematik at University of Osnabruck, Germany

10/1986 - 09/1988,
04/1989 - 09/1991
Student Assistent (46h/month) at the Computer Center of the University of Osnabruck
10/1988 - 04/1989 Exchange student at the Department of Applied Mathematics, University of Hull, England 
(fluid dynamics and partial differential equations, B.Sc. level)
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Publications

2014

2013

 

 

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

2002

  • Tulet P, Suhre K, Mari C, Solmon F, Rosset R. Mixing of boundary layer and upper tropospheric ozone during a deep convective event over Western Europe. Atmospheric Environment 2002. Vol. 36 pp. 4491-4501.

1994 - 2000


Theses


Patent Applications


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Research

Human metabolic individuality in biomedical and pharmaceutical research

  • Genome-wide association studies (GWAS) have identified many risk loci for complex diseases, but effect sizes are typically small and information on the underlying biological processes is often lacking. Associations with metabolic traits as functional intermediates can overcome these problems and potentially inform individualized therapy. In several ground-breaking studies since 2008, we reported comprehensive analyses of genotype-dependent metabolic phenotypes using a GWAS with targeted and non-targeted metabolomics in blood and urine. We identified until now over 150 genetic loci associated with blood metabolite concentrations, of which many show effect sizes that are unusually high for GWAS and account for up to 60% differences in metabolite levels per allele copy. Our associations provide new functional insights for many disease-related associations that have been reported in previous studies, including those for cardiovascular and kidney disorders, type 2 diabetes, cancer, gout, venous thromboembolism and Crohn’s disease. These studies advance our knowledge of the genetic basis of metabolic individuality in humans and generate many new hypotheses for biomedical and pharmaceutical research.

Here is a list of all studies that we published so far on the discovery of new genetically influenced metabotypes (GIMs):

  • Gieger, C, Geistlinger, L, Altmaier, E, Hrabé de Angelis, M, Kronenberg, F, Meitinger, T, Mewes, HW, Wichmann, HE, Weinberger, KM, Adamski, J, Illig, T, Suhre K, Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum , PLoS Genetics, 4(11):e1000282, 2008. [This paper reports the first GWAS with metabolomics and establishes the concept of GIMs] 
  • Illig, T, Gieger, C, Zhai, G, Römisch-Margl, W, Wang-Sattler, R, Prehn, C, Altmaier, E, Kastenmüller, G, Kato, BS , Mewes, HW, Meitinger, T, Hrabé de Angelis, M, Kronenberg, F, Soranzo, N , Wichmann, HE, Spector, TD, Adamski, J, Suhre, K, A genome-wide perspective of genetic variation in human metabolism, Nature Genetics, 42:137-141, 2010, doi:10.1038/ng.507. [This paper describes the first fully powered GWAS with targeted metabolomics/lipidomics]
  • Suhre K., Wallaschofski H., RafflerJ., Friedrich N., Haring R., Michael K., Wasner C., Krebs A., Kronenberg F., Chang D., Meisinger C., Wichmann H.-E., Hoffmann W., Völzke H., Völker U., Teumer A., Biffar R., Kocher T., Felix S.B., Illig T., Kroemer H.K., GiegerC., Römisch-Margl W., Nauck M., A genome-wide association study of metabolic traits in human urine Nature Genetics, 43:565-569, 2011. [This paper describes the first GWAS with NMR-derived metabolites in urine]
  • Suhre K, Shin S-Y, Petersen A-K, Mohney RP, Meredith D, Wagele B, Altmaier E, CARDIoGRAM, Deloukas P, Erdmann J, Grundberg E, Hammond CJ, de Angelis MH, Kastenmüller G, Kottgen A, Kronenberg F, Mangino M, Meisinger C, Meitinger T, Mewes H-W, Milburn MV, Prehn C, Raffler J, Ried JS, Romisch-Margl W, Samani NJ, Small KS, Erich Wichmann H, Zhai G, Illig T, Spector TD, Adamski J, Soranzo N, Gieger C. Human metabolic individuality in biomedical and pharmaceutical research. Nature, 477:54-60, 2011. [This paper describes a GWAS with the most comprehensive set of non-targeted metabolomics at the time and reports 37 GIMs]
  • Krumsiek J, Suhre K, Evans AM, Mitchell MW, Mohney RP, Milburn MV, Wägele B, Römisch-Margl W, Illig T, Adamski J, Gieger C, Theis FJ, Kastenmüller G., Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information. PLoS Genetics, 8:e1003005, 2012. [This paper uses a GWAS with metabolites of unknown biochemical identity to reveal their biochemical properties]
  • Raffler J, Römisch-Margl W, Petersen AK, Pagel P, Blöchl F, Hengstenberg C, Illig T, Meisinger C, Stark K, Wichmann HE, Adamski J, Gieger C, Kastenmüller G, Suhre K, Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma. Genome Med., 5:13, 2013. [This paper reports a GWAS with NMR peaks and relates them to MS-derived metabotypes]
  • Petersen AK, Zeilinger S, Kastenmüller G, Römisch-Margl W, Brugger M, Peters A, Meisinger C, Strauch K, Hengstenberg C, Pagel P, Huber F, Mohney RP, Grallert H, Illig T, Adamski J, Waldenberger M, Gieger C, Suhre K, Epigenetics meets metabolomics: An epigenome-wide association study with blood serum metabolic traits, Hum Mol Genet., 23:534-545, 2014. [This paper describes the first EWAS with metabolomics]
  • Shin SY, Fauman EB, Petersen AK, Krumsiek J, Santos R, Huang J, Arnold M, Erte I, Forgetta V, Yang TP, Walter K, Menni C, Chen L, Vasquez L, Valdes AM, Hyde CL, Wang V, Ziemek D, Roberts P, Xi L, Grundberg E, The MuTHER Consortium, Waldenberger M, Richards JB, Mohney RP, Milburn MV, John SL, Trimmer J, Theis FJ, Overington JP, Suhre K*, Brosnan MJ*, Gieger C*, Kastenmüller G*, Spector TD*, Soranzo N*, An atlas of genetic influences on human blood metabolites, Nature Genetics, 46:543-550, 2014. [This paper reports the largest GWAS with non-targeted metabolomics to date and describes 145 GIMs, each of them telling its own biological story]

 

 

 

 

 

genetically determined metabotypes

 

Read the WCMC-Q press release for our Nature (2011) paper

 

 

DATA ACCESS (Shin et al., 2014):

http://www.gwas.eu

 

http://mips.helmholtz-muenchen.de/proj/GWAS/gwas/gwas_server/images/logo_ti.png

 

DATA ACCESS (Suhre et al., 2011):

HMGU server [WCMC-Q mirror]

 

 

 

http://t2.gstatic.com/images?q=tbn:ANd9GcRU2skW4Vmlyp0RumtvSxlBwJAd8O003CgMlQMfS3xR-SYkJZOtWw

 

Watch Al Jazeera Interview

 

Read the WCMC-Q press release for our Nature Genetics (2014) paper

 

Webservers for Genomics, Metabolomics, and Protein Structure Analyses

 

The following Web Server are supported or were co-developped by my group:

  • ElNemo: The Elastic Network Model
    This server is the Web-interface to the Elastic Network Model (ENM), a fast and simple way for computing the low frequency normal modes of a macromolecule.

 

 

 

 

 

 

 

 

http://mips.helmholtz-muenchen.de/proj/GWAS/gwas/gwas_server/images/logo_ti.png

 

 

 

 


 

BOOK: Genetics Meets Metabolomics:
from Experiment to Systems Biology

  • Summary: Unlike previous books published on metabolomics, this book switches the focus from experimental questions and technical challenges, to the application of metabolomics with an emphasis on the underlying genetics. The chapters provide a thorough basis for the understanding of the underlying experimental techniques, concepts and potential biomedical applications of this exciting field. The interdisciplinary approach of this book addresses a wide readership, and contains educational aids for anyone not familiar with a particular area of metabolomics. The area of research where genetics and metabolomics meet is likely to represent a field where systems biology shall prosper highly in the years to come.
  • Content: Pre-conditions for high quality biobanking in large human epidemiological cohorts for metabolomics and other -omics studies.- Assay Tools for Metabolomics.- Statistical methods in genetic and molecular epidemiology and their application in studies with metabolic phenotypes.- Ultrahigh resolution mass spectrometry based non-targeted microbial metabolomics.- etabolomic systems biology of protozoan parasites.- Mouse genetics and metabolic mouse phenotyping.- Metabolomics in animal breeding.- Metabolomics applications in human nutrition.- Metabolomics for the individualized therapy of androgen deficiency syndrome in male adults.- Systems biology resources arising from the human metabolome project.- Understanding cancer metabolism through global metabolomics.- Genetic and metabolic determinants of fatty acid chain length and desaturation, their incorporation into lipid classes and their effects on risk of vascular and metabolic disease.- Mapping metabolomic quantitative trait loci (mQTL) – A link between metabolome-wide association studies and systems biology.- Metabolic traits as intermediate phenotype.- Genome-wide association studies with metabolomics.- Systems biology meets metabolism.

book cover

Link to Springer

Link to Amazon.com

Read this book online

 

Establishing world leadership in date palm research in Qatar

  • Weill Cornell Medical College in Qatar won the first award in the Qatar National Research Fund (QNRF) Exceptional Proposal program with Dr. Karsten Suhre, Professor of Physiology and Director of the Bioinformatics Core, and Dr. Joel Malek, Director of the Genomics Core, awarded a five-year grant of $US4.5 million for their project Establishing World Leadership in Date Palm Research in Qatar.
  • The proposal combines two innovative technologies that are well established at WCMC-Q, genomics and metabolomics, in an interdisciplinary approach to date palm research, addressing major challenges of the field. WCMC-Q is collaborating with the Ministry of Environment’s Biotechnology Center in Qatar, the Helmholtz Centre in Munich, the French National Institute for Agricultural Research, and the European Institute for Research and Development.
  • The goal of the project is to better understand date palm biology and link the genetics of the date palm to date palm characteristics such as fruit color, flavor and ability to resist disease or environmental stress.
  • Go to the dactylifera.org web-site

The following studies report results related to this project:

 

 

Karsten Suhre and Joel Malek with a date palm

Read the WCMC-Q press release

Read the QNRF press release

 

 

Diabetes Research - a non-invasive marker for diabetes screening

 

  • In most ethnicities at least a quarter of all cases with diabetes is assumed to be undiagnosed. Screening for diabetes using saliva has been suggested as an effective approach to identify affected individuals. The objective of this study is to identify a non-invasive metabolic marker of type 2 diabetes in saliva. In a case-control study of type 2 diabetes, we used a clinical metabolomics discovery study to screen for diabetes-relevant metabolic readouts in saliva, using blood and urine as a reference. With a combination of three metabolomics platforms based on non-targeted mass spectrometry we examined 2,178 metabolites in saliva, blood plasma, and urine samples from 188 subjects with type 2 diabetes and 181 controls of Arab and Asian ethnicities. We found a strong association of type 2 diabetes with 1,5-anhydroglucitol (1,5-AG) in saliva (p=3.6×10−13). Levels of 1,5-AG in saliva highly correlated with 1,5-AG levels in blood and inversely correlated with blood glucose and HbA1c levels. These findings were robust across three different non-Caucasian ethnicities (Arabs, South Asians, and Philippines) irrespective of body mass index, age and gender. Clinical studies have already established 1,5-AG in blood as a reliable marker of short-term glycemic control. Our study suggests that 1,5-AG in saliva can be used in national screening programs for undiagnosed diabetes, which are of particular interest for Middle Eastern countries with young populations and exceptionally high diabetes rates.
  • Mook-Kanamori DO, El-Din Selim MM, Takiddin AH, Al-Homsi H, Al-Mahmoud KA, Al-Obaidli A, Zirie MA, Rowe J, Yousri NA, Karoly ED, Kocher T, Sekkal Gherbi W, Chidiac OM, Mook-Kanamori MJ, Abdul Kader S, Al Muftah WA, McKeon C, Suhre K, 1,5-anhydroglucitol in saliva is a non-invasive marker of short-term glycemic control, J Clin Endocrinol Metab, [Epub ahead of print], 2014. 

 

 

 

Read the WCMC-Q press release

 

 

Ethnic differences in skin autofluorescence - a predictor of cardiovascular risk

 

  • Advanced glycation end products (AGEs) have been shown to be a predictor of cardiovascular risk in Caucasian subjects. In this study we examine whether the existing reference values are useable for non-Caucasian ethnicities. Furthermore, we assessed whether gender and smoking affect AGEs. AGEs were determined by a non-invasive method of skin auto-fluorescence (AF). AF was measured in 200 Arabs, 99 South Asians, 35 Filipinos and 14 subjects of other/mixed ethnicity in the Qatar Metabolomics Study on Diabetes (QMDiab). Using multivariate linear regression analysis and adjusting for age and type 2 diabetes, we assessed whether ethnicity, gender and smoking were associated with AF. The mean AF was 2.27 arbitrary units (AU) (SD: 0.63). Arabs and Filipinos had a significant higher AF than the South Asian population (0.25 arbitrary units (AU) (95% CI: 0.11–0.39), p = 0.001 and 0.34 (95% CI: 0.13–0.55), p = 0.001 respectively). Also, AF was significantly higher in females (0.41 AU (95% CI: 0.29–0.53), p < 0.001). AF associated with smoking (0.21 AU (95% CI: 0.01–0.41), p = 0.04) and increased with the number of pack-years smoked (p = 0.02). This study suggests that the existing reference values should take ethnicity, gender and smoking into account. Larger studies in specific ethnicities are necessary to create ethnic- and gender-specific reference values.
  • Mook-Kanamori MJ, Selim MM, Takiddin AH, Al-Homsi H, Al-Mahmoud KA, Al-Obaidli A, Zirie MA, Rowe J, Gherbi WS, Chidiac OM, Kader SA, Al Muftah WA, McKeon C, Suhre K, Mook-Kanamori DO, Ethnic and gender differences in advanced glycation end products measured by skin auto-fluorescence. Dermato-Endocrinology, 5:325-330, 2013.

 

 

 

Read the WCMC-Q press release

 

 

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Projects developped at Helmholtz Center Munich (HMGU)


Metabolomics research
  • At the Helmholtz Center Munich - German Research Center for Environmental Health (HMGU), I started a research program on genetically determined human metabotypes and their link to complex disease. Metabolomics studies in animal models, such as mice and bovine are used in complement to studies in a human population. As a bioinformatician, I combine data from different sources, many of them from HelmholtzMuenchen instruments, such as targeted quantitative metabolomics from a API Q TRAP 4000, non-targeted metabolomics from a Bruker 12 Tesla APEX FT-ICR, and genotyping information using Affymetrix 500k and 6.0 GeneChip arrays on the KORA population.
  • I have set up a group in metabolic research, with partners from the Helmholtz Zentrum München institutes GAC (J. Adamski), EPI (T. Illig), and IOEC (P. Schmitt-Kopplin). Our group is providing different bioinformatics ressources, which are available through this metabolomics web server. On that site, a Wiki for the metabolic initiative MetaP is available for registered users.
  • We have organized the conference Metabolomics & More : The Impact of Metabolomics on the Life Sciences, which will be held on March 10-12, 2010 in Freising-Weihenstephan, Germany.
  • MassTRIX: Mass TRanslator into Pathways is a web server for the annotation of high precision mass spectrometry data. It is available at www.masstrix.org.

Conference



metaP ressources



MassTRIX.org







German Centre for Diabetes Research - DZD e.V.
  • The "Deutsches Zentrum fuer Diabetesforschung e.V." (DZD) is an intertdisciplinary cooperation of the Helmholtz Association and the Leibniz Association with strong contributions from the University of Tuebingen and the University Clinic Dresden. The managing office is at the Helmholtz Centre Munich.

Gani_Med
  • Greifswald Approach to Individualized Medicine (BMBF-research project). The objective of Gani_Med is to use state-of-the-art diagnostics and novel therapeutic interventions that take into account the specific requirements and characteristics of the individual patient in order to increase the effectiveness of treatments, avoid unwanted adverse reactions and significantly reduce health care costs.

SysMBo
  • Systems Biology of Metabotypes (BMBF-research project). SysMBo is an interdisciplinary research consortium aiming to unravel the complex relations between genetic predisposition, environmental stimuli and disease. With the help of high-throughput metabolite profiling and powerful modelling tools, the researchers take a system based approach in order to understand the complex interplay between numerous factors leading to a pathophenotype.

Genome Analysis Centre (GAC)
  • The Metabolomic Platform (metaP) is a scientific interdisciplinary cooperation of Institutes of the Helmholtz Zentrum München. The activities include both profiling (analyses of all measurable analytes to identify differences) and targeted analyses (quantification of a chosen set of analytes). These activities are possible by the unique contributions of participating Helmholtz Zentrum München institutes in the GAC.

What are genetically determined metabotypes?

Common genetic polymorphisms induce major differentiations in the metabolic make-up of the human population. We conducted a genome-wide association study with metabolomics, identifying genetic variants in genes involved in the breakdown of fats (Gieger et al., PLoS Genetics, 2008). The resulting differences in metabolic capacity can affect individuals' susceptibility to complex diseases such as diabetes and hyperactivity. In the rapidly evolving field of metabolomics, scientists aim to measure all endogenous metabolites in a cell or body fluid. These measurements provide a functional readout of the physiological state of the human body. Investigation into these so-called "genetically determined metabotypes" in their biochemical context may help determine the pathogenesis of common diseases and gene-environment interactions. We identified four single nucleotide polymorphisms (SNPs) located in genes coding for well-characterized enzymes of the lipid metabolism. Individuals with different genotypes in these genes have significantly different metabolic capacities with respect to the synthesis of some polyunsaturated fatty acids, the beta-oxidation of short- and medium-chain fatty acids and the breakdown of triglycerides. By simultaneous measurements of both SNPs and serum concentrations of endogenous metabolites, the researchers determined the metabolome of several hundred healthy individuals and compared it to their genetic inheritance. The results suggest that most individuals carry one or more risk alleles in their genetic inheritance that may determine a certain medical phenotype, the response to a given drug treatment, or the reaction to a nutritional intervention or environmental challenge. These findings may lead to more targeted approaches to health care based on a combination of genotyping and metabolic characterization. To achieve this goal, it will be necessary to identify the major genetically determined metabotypes and their association to complex diseases.

A much larger study has been published in Nature Genetics (Illig, Gieger et al., 2010). This study identifies a number of new genetically determined metabotypes.

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Projects formerly developped at IGS-CNRS


Normal mode analysis
The Elastic Network Model

Docking - In Silico screening

GFscore
Mimivirus genome analysis




Repeat Protein Analysis
  • CaMBOT probing led to the isolation of a novel calmodulin binding protein cmbB in the social amoeba Dictyostelium discoideum. Structural and bioinformatic analyses reveal that the cmbB protein is almost entirely comprised of tandem repeats of an IP22 motif, which is a more precise representation of the previously identified FNIP repeat. cmbB also appears to share structural homology to YopM, from the plague bacterium Yersenia pestis, and its closest homologues are found in Mimivirus.
  • Collaboration with Prof. Danton O'Day.
  • REF: O'Day et al., BBRC, 2006.


PhydBac - phylogenomic display of bacterial genes



CaspR: Automated molecular replacement using homology modelling
  • CaspR is a web-server for automated molecular replacement by screening a large number of homology models for a potential solution.
  • The method that is implemented in CaspR was first used to solve the crystal structure of the E. coli protein YecD (PDB-id 1J2R).
  • The implementation of this method as a web-based server is part of the PhD research work of Jean-Baptiste Claude
  • REF: Claude et al., NAR, 2004.

3D-Coffee: multiple sequence-structure alignments with T-Coffee

Microarray data analysis

Structural biology

FusionDB - a database of prokaryotic gene fusion events

Genomic correlates of hyperthermostability
  • Statistical (principal component) analysis of the amino acid composition of most sequenced bacterial genomes. We show that the CHA-POL criteria (replacement of polar by charges residues in thermophilic organisms) is an optimal criteria to discriminate meso-philic from thermophilic proteins.
  • REF: Suhre and Claverie, J. Biol. Chem., 2003

Bacterial genome sequencing and annotation
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Past activities

A209: The new Mercedes CLK convertible
the new Mercedes CLK convertible
ACE
Aerosol Characterization Experiments 1, 2, Asia.
  • Coupled physico-chemical modelling of ACE-1 and ACE-2 Lagrangian experiments
  • Co-ordinator of the modelling activities in ACE-2 (IntegModel)
  • Principal investigator in the ACE-2 EU project CloudyColumn
  • Preparatory studies for Lagrangian experiments in ACE-Asia
MOZAIC
Measurement of Ozone, Water Vapor, Carbon Monoxide and Nitrogen Oxides by Airbus-In-Service Aircraft.
  • Troposphere-stratosphere exchange in the tropics
  • Feasability studies of an aerosol measurement device for MOZAIC
MesoNH
The non-hydrostatic mesoscale atmospheric model of the French atmospheric research community.
  • Responsible of the atmospheric chemistry module MesoNH-chemistry (MNHC)
  • 3-D mesoscale and large eddy simulations of ACE-2 situations
Quantum field theory (diploma work)
Das Feld am Punkt im auesseren elektromagnetischen Feld
  • The Fermifield in an external electro-magnetic field will be defined as a sesquilinear form at one point without using test functions. It will be shown to satisfy the Dirac-equation and to be local in an appropriate sense. Moreover, based on the field at one point von-Neuman algebrae will be defined that are identical to the smeared field. This fact is not a straight forward deduction as the field is not translationally invariant. The twisted duality R(O) = R(O')t' will be proven in this work.
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Last modified on Sunday, 17-Aug-2014 08:48:14 AST