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Manchester Centre for Integrative Systems Biology

Dr Warwick (Rick) Dunn


 

Address

 

(Room 2.002)

Manchester Centre for Integrative Systems Biology

Manchester Interdisciplinary Biocentre

131 Princess Street

Manchester M1 7DN

UK

 

Telephone

 

+44 (0) 161 30 65146

 

Fax

 

+44 (0) 161 30 64556

 

email

 

Warwick.Dunn@manchester.ac.uk

Rick Dunn

 

 

 

 

 

 

 

Research interests

 

When you measure what you are speaking about and express it in numbers, you know something about it, but when you cannot express it in numbers your knowledge is of a meagre and unsatisfactory kind.

(Lord Kelvin, early 20th century)

 

Current research interests: Metabolomics

 

Rick's research goals focus on the systems biology investigations of microbial and mammalian systems, specifically the application of metabolomics to these disciplines and the development of analytical instrumentation and methodologies to fulfill these goals.

 

Metabolomics is focussed on the holistic and data-driven investigation of the quantitative collection of low molecular weight organic and inorganic compounds present in biological systems. This collection of endogenous and exogenous metabolites is defined as the metabolome. Endogenous metabolites can be biochemically synthesized or catabolised within the system and exogenous metabolites are acquired from the external environment (for example, food nutrients and drugs) or from co-habiting species (for example, gut microbiome). A range of experimental strategies are employed to investigate the metabolome including metabolic profiling (untargeted analysis), targeted analysis and metabolite fingerprinting, each with different advantages and disadvantages. Both the intracellular and extracellular (metabolic footprint) metabolomes can be investigated to increase our understanding of biological systems. Metabolomes are physically and chemically complex and challenging to investigate.

 

My research goals involve the development of workflows (or metabolomic pipelines), instrumental technologies and analytical methodologies to enable the detailed and reproducible investigation of microbial and mammalian metabolomes, so to increase the biological and mechanistic understanding of these systems. Biological systems studied include baker's yeast Saccharomyces cerevisiae and mammals. The workflows extend from sampling of metabolomes to sample preparation, acquisition of analytical data, processing of raw data and the conversion of data to biological knowledge. A specific interest is the provision of quality in metabolomic experiments, including experimental design and the development of quality control (QC) sample use. No single analytical platform can detect all metabolites and the application of multiple platforms is recommended. My expertise has allowed me to develop and exploit a range of mass spectrometric platforms for the investigation of metabolomes including gas chromatography-time of flight-mass spectrometry (GC-ToF-MS), comprehensive GCxGC-ToF-MS, direct infusion mass spectrometry (DIMS) and Ultra Performance Liquid Chromatography-mass spectrometry (UPLC-MS). These technologies have been developed to produce valid and reproducible datasets for both short-term and long-term metabolomic studies. I work with Professor Douglas Kell and Professor Roy Goodacre in MCISB and previously in the Bioanalytical Sciences group. My research interests include:

 

1. Systems biology investigation of baker's yeast Saccharomyces cerevisiae

 

At the Manchester Centre for Integrative Systems Biology (MCISB) we are developing new systems biology-focused experimental and computational technologies to investigate and quantitatively model the metabolism of baker's yeast, Saccharomyces cerevisiae. This involves the development of mathematical models, acquisition of experimental data and the integrated fusion of models and data in an iterative relationship to construct, test and validate quantitative metabolic models. My role is focussed on the development, validation and application of targeted analytical methodologies to provide the absolute quantification of metabolites present in the intracellular and metabolic footprints of yeast under defined and reproducible growth conditions (a typical example can be seen here). Previous research with Professor Douglas Kell and Dr Irena Spasic involved a large-scale metabolic footprint investigation of single gene deletant mutants of S. cerevisiae.

 

2. Development and exploitation of mass spectrometric technologies for metabolomic investigations

 

As an analytical chemist my primary objective is to apply technological platforms to provide reproducible and 'fit for purpose' data for research goals. At Manchester (and previously at The University of Sheffield) I am developing mass spectrometric platforms for metabolic profiling and metabolite fingerprinting. These have included optimisation of analytical platforms to maximise the number of metabolites detected and development of methodologies that provide reproducible data appropriate for studying small changes in metabolic profiles. The introduction of new analytical technologies including GC-TOF-MS, comprehensive GCxGC-TOF-MS, UPLC and the hybrid LTQ-Orbitrap mass spectrometer (all applied at Manchester) have enabled researchers to detect and identify larger fractions of a range of metabolomes. A separate problem being addressed at Manchester is the identification of metabolites, essential to allow the conversion of analytical data to biological knowledge. Identification of metabolites can be performed using a number of different approaches, including the development of mass spectral libraries with authentic standards and elucidation of metabolite identifications from accurate mass, isotope patterns and fragmentation mass spectra. We are currently constructing GC-EI-TOF-MS retention index/mass spectral libraries employing LECO GC-ToF-MS instruments and retention time/accurate mass/CID fragmentation libraries employing UPLC coupled to a LTQ/Orbitrap hybrid mass spectrometer. Quality assurance and the application of quality control (QC) samples in metabolomics have been developed in Manchester.

 

3. Investigation of the metabolomes of "healthy" and "diseased" humans

 

The metabolome is an ideal system to investigate the phenotypes of humans. At Manchester we are studying the variability observed in the metabolomes of healthy individuals and the disease-independent changes caused by diet, gender, age and lifestyle (as investigated in the HUSERMET project). We are also investigating differences in metabolic profiles associated with diseases including pre-eclampsia eclampsia and IUGR, heart disease, kidney disease & transplantation and diabetes. These differences can be applied to define risk factors or as prognostic or diagnostic biomarkers of disease and also enable a mechanistic model of disease (pathophysiology) to be deduced. Serum/plasma, urine and tissue are investigated. I work closely with a number of researchers at Manchester including Dr David Broadhurst and Dr Marie Brown.

 

My professional Curriculum Vitae can be seen here.

 

 

Publications

 

Reviews

 

Dunn, W. B. (2008)

Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes.

Physical Biology, 5, 011001

 

Samuel, J-l., Schaub, M.C., Zaugg, M., Mamas, M., Dunn, W.B. et al. (2008)

Genomics in cardiac metabolism.

Cardiovascular research, 79, 218-227

 

Ellis, D. I., W. B. Dunn, et al. (2007)

Metabolic fingerprinting as a diagnostic tool.

Pharmacogenomics, 8, 1243-1266

 

Dunn, W.B., Bailey, N.J.C. and Johnson, H.E. (2005)

Measuring the metabolome: current analytical technologies.

Analyst, 130, 606-625

 

Dunn, W.B. and Ellis, D.I. (2005)

Metabolomics: current analytical platforms and methodologies.

TrAC: Trends Analytical Chemistry, 24, 285-294

 

Kell, D.B., Brown, M., Davey, H.M., Dunn, W.B., Spasic, I and Oliver, S.G. (2005)

Metabolic footprinting and systems biology: The medium is the message.

Nature Reviews Microbiology, 3, 557-565

 

Brown, M., Dunn, W.B., Ellis et al. (2005)

A metabolome pipeline: from concept to data to knowledge.

Metabolomics, 1, 39-51

 

Goodacre, R., Vaidyanathan, S., et al. (2004)

Metabolomics by numbers: acquiring and understanding global metabolite data.

Trends Biotechnology, 24, 245-253

 

 

Microbial metabolomics

 

Herrgard MJ, Swainston N, Dobson P, Dunn WB, et al. (2008)

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Nature Biotechnology, 26, 1155-1160

 

Winder C.L., Dunn W.B., Schuler S., et al. (2008)

Global metabolic profiling of Escherichia coli cultures: An evaluation of methods for quenching and extraction of intracellular metabolites.

Analytical Chemistry, 80, 2939-2948

 

MacKenzie, D.A., Defernez, M., Dunn, W.B. et al. (2008)

Relatedness of clinical, probiotic and commercial isolates of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics.

Yeast, 25, 501-512

 

Peiris, D., Dunn, W.B., Brown, M., Kell, D.B. and Hedger, J. (2008)

Metabolite profiles of interacting mycelial fronts differ for the wood decay basidiomycete fungi Stereum hirsutum, Coprinus micaceus and Coprinus disseminatus.

Metabolomics, 4, 52-62

 

Castrillo JI, Zeef LA, et al. (2007)

Growth control of the eukaryote cell: a systems biology study in yeast.

Journal of Biology, 6, art 4

 

Pope, G.A., Mackenzie, D.A., et al. (2007)

Metabolic footprinting as a tool for discriminating between brewing yeasts.

Yeast, 24, 667-679

 

 

Mammalian metabolomics

 

Dunn, W.B., Brown, M., Worton, S.A., et al. (2009)

Changes in the metabolic footprint of cultured villous trophoblast identifies metabolic disturbances related to hypoxia and pre-eclampsia.

Placenta, in press

 

Heazell, A.E.P., Brown, M., Dunn, W.B. et al. (2008)

Analysis of the Metabolic Footprint and Tissue Metabolome of Placental Villous Explants Cultured at Different Oxygen Tensions Reveals Novel Redox Biomarkers.

Placenta, 29, 691-698

 

Kenny LC, Broadhurst D, Brown M, Dunn WB, et al. (2008)

Detection and Identification of Novel Metabolomic Biomarkers in Preeclampsia.

Reproductive Sciences, 15, 591-598

 

Dunn, W. B., Broadhurst, D., et al. (2008)

A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols.

Int J Epidemiol, 37, i23-i30.

 

Dunn, W.B., Broadhurst, D.I., et al. (2007)

Serum metabolomics reveals many novel metabolic markers of heart failure, including pseudouridine and 2-oxoglutarate.

Metabolomics, 3, 413-426

 

Underwood, B.R., Broadhurst, D., Dunn, W.B., Ellis, D.I., Michell, A.W., Vacher, C., Mosedale, D.E., Kell, D.B., Barker, R.A., Grainger, D.J. and Rubinsztein, D.C. (2006)

Huntington disease patients and transgenic mice have similar pro-catabolic serum metabolite profiles,

Brain, 129, 877-886

 

Kenny, L.C., Dunn, W.B., et al. (2005)

Novel biomarkers for preeclampsia detected using metabolomics and machine learning,

Metabolomics, 1, 227

 

 

Instrument and methodology development

 

Begley, P., Francis-McIntyre, S., Dunn, W.B., et al. (2009)

Development and Performance of a Gas Chromatography-Time-of-Flight Mass Spectrometry Analysis for Large-Scale Nontargeted Metabolomic Studies of Human Serum.

Analytical Chemistry, in press

 

Allwood, J.W., Erban, A., de Koning, J., Dunn, W.B., et al. (2009)

Inter-laboratory reproducibility of fast gas chromatography - electron impact - time of flight mass spectrometry (GC-EI-TOF/MS) based plant metabolomics.

Metabolomics, in press

 

Biais B, Allwood JW, Deborde C, et al. (2009)

1H NMR, GC-EI-TOFMS, and data set correlation for fruit metabolomics: application to spatial metabolite analysis in melon.

Analytical Chemistry, 81, 2884-94

 

Zelena E, Dunn WB, Broadhurst D, et al. (2009)

Development of a Robust and Repeatable UPLC-MS Method for the Long-Term Metabolomic Study of Human Serum.

Analytical Chemistry, 81, 1357-1364

 

Brown M, Dunn WB, Dobson P, et al. (2009)

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics.

The Analyst, 134, 1322-1332

 

Dunn, W.B., Broadhurst, D., et al. (2008)

Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system.

J. Chromat. B, 871, 288-298

 

Winder, C.L., Dunn, W.B., et al. (2008)

Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites.

Anal Chem., 80, 2939-48

 

Lu, H., W. B. Dunn, et al. (2008)

Comparative evaluation of software for deconvolution of metabolomics data based on GC-TOF-MS.

Trac-Trends in Analytical Chemistry, 27, 215-227

 

O’Hagan, S.O., Dunn, W.B., et al. (2007)

Closed-loop, multiobjective optimization of two-dimensional gas chromatography/mass spectrometry for serum metabolomics.

Analytical Chemistry, 79, 464-476

 

Spasic, I., Dunn, W.B., Velarde, G., Tseng, A., Jenkins, H., Hardy, N., Oliver, S.G. and Kell, D.B. (2006)

MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics.

BMC Bioinformatics, 7, 281

 

Vaidyanathan, S., Jones, D., Broadhurst, D., Ellis, J., Jenkins, T., Dunn, W.B., Hayes, A., Burton, N., Oliver, S.G., Kell, D.B. and Goodacre, R. (2005)

A laser desorption ionization mass spectrometry approach for high throughput metabolomics.

Metabolomics, 1, 243-250

 

Dunn, W.B., Overy, S. and Quick, W.P., (2005)

Evaluation of Automated Electrospray-TOF Mass Spectrometry for Metabolite Fingerprinting.

Metabolomics, 1, 137-148

 

O’Hagan, S., Dunn, W.B., et al. (2005)

Closed-loop, multiobjective optimization of analytical instrumentation: gas chromatography/time-of-flight mass spectrometry of the metabolomes of human serum and of yeast fermentations.

Anal. Chem, 77, 290-303

 

 

Relevant websites

 

The websites and publications detailed below are not intended to be comprehensive, are not in any specific order of preference and are provided as an initial portal to the subjects of metabolomics and mass spectrometry.

 

Rick's list of recommended reading can be seen here.

 

Metabolomics and Systems Biology at Manchester

 

Professor Douglas Kell's group website
Manchester Centre for Integrative Systems Biology
The HUSERMET project
Laboratory for Bioanalytical Spectroscopy

 

Portals to Metabolomics and Chemistry

 

The Metabolomics Society
The Royal Society of Chemistry
Metabolomics journal
The Golm Metabolome Database
The Metabolomics Fiehn Lab
Metabolomics at The Scripps Centre for Mass Spectrometry
The Human Metabolome Database including DrugBank and FoodDB
MetRO at Rothamsted
Quantitative Biology and Bioinformatics (Matej Orešić)
MassBank.jp
Comprehensive Yeast Genome Database
KEGG
Reactome
BioCyc
InChI
ChEBI
PubChem
ChemSpider

 

Mass Spectrometry Instrument Manufacturers

 

LECO
Anatune Ltd
Waters
Bruker
Agilent's metabolomics lab
Applied Biosystems
ThermoFisher Electron ThermoFisher Electron

 

Mass spectrometry based websites

 

British Mass Spectrometry Society
American Society for Mass Spectrometry
Michael Barber Centre for Mass Spectrometry at The University of Manchester
Spectroscopy Now
i-mass
Ion source
AMDIS (Automated Mass Spectral Deconvulotion and Identification Software)
XCMS
List of accurate atomic weights and isotope information

 

Other websites

 

School of Chemistry, University of Manchester
Manchester Interdisciplinary Biocentre
BBSRC
EPSRC
UoM webmail
UoM mail manager
Google
Trainline
Animal and Plant Sciences, University of Sheffield

 

 

Interests

 

Good ale and food, sport, Sheffield United FC season ticket holder, walking, gardening.

 

Campaign for Real Ale
Everything to learn about Sheffield (UK)
Sheffield United FC (greatest football club ever!)
SUFC Annie's Song
Yorkshire County Cricket Club
Everything to learn about Manchester (UK)
Peak District National Park
Walks in The Peak District
Photos of the Peak District
Lake District National Park
Walks in the Lake District
Photos of the Lake District
Yorkshire Dales National Park
Walks in the Yorkshire Dales
Photos of the Yorkshire Dales
Snowdonia National park
Walks in the Snowdonia National Park
Pictures of the Snowdonia National Park
BBC Weather
BBS Sport
BBC Radio One
Dilbert
Rock Tavern
Royal Horticultural Society
National Trust
Trainline
Manchester Online
Meerkats