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PROGRAM
Sunday, December 7, 2003
5:00-6:30 Early Registration, Poster and Exhibit Set-up
Monday, December 8, 2003
8:00 Registration, Poster and Exhibit Viewing, Morning coffee
Perspectives on Metabolic Profiling
9:00 Welcome by Session Chairperson
Dr. Rima Kaddurah Daouk, Metabolon and Dana Farber Cancer Institute
9:15 Metabonomics at NCTR
Dr. Richard D. Beger, Division of Chemistry, National Center for
Toxicological Research, Food and Drug Administration
The National Center for Toxicological Research (NCTR) is initiating an
intensive NMR-based metabonomics research program and has developed a
metabonomics research laboratory. The NCTR and FDA goals of metabonomics
research and the status of rat and human ongoing metabonomics research will be
addressed in this presentation-including a systems biology approach on
elucidating the bimolecular mechanisms of hepatotoxic N-acetyl-p-aminophenol
(acetaminophen; APAP) based on differences in omic data from the non-toxic
N-acetyl-m-aminophenol (AMAP) structural congener to APAP. Metabonomics analysis
of serum from rats multiply dosed with TCDD will also be discussed.
9:45 Global Differential Expression Profiling
for Metabolic Biomarker Discovery: Advances and Challenges
Dr. Haihong Zhou, Research Scientist, Chemistry, SurroMed, Inc.
Metabolic profiles of bodily fluids such as plasma, cerebrospinal fluid and
urine reflect both normal variation and the physiological impact of disease and
pharmaceuticals on organ systems. We are tracking and quantifying hundreds to
thousands of low-molecular-weight metabolites in these body fluids collected
from healthy and diseased populations. This presentation will report the
advances of our technology platforms for large-scale metabolic profiling using
GC-MS and LC-MS, and the application of this approach to clinical studies of
multiple sclerosis and rheumatoid arthritis.
10:15 Poster and Exhibit Viewing, Refreshment
Break
10:50 The Intersection of Structural Genomics
and Metabolic Profiling
Dr. John Orban, Associate Professor, Center for Advanced Research in
Biotechnology, University of Maryland Biotechnology Institute
Structure-based approaches such as X-ray crystallography and NMR
spectroscopy are currently being used to gain insights into the functions of
poorly understood proteins in Haemophilus influenzae, typically with sequence
homologues in a wide variety of organisms from bacteria to eukaryotes. This
approach often provides structures that suggest an interaction with a small
molecule by the nature of the fold and the presence of suitable cavities which
may serve as binding sites. Structural information has been combined with small
molecule ligand screening to narrow down potential biochemical functions within
metabolic pathways (Supported by NIH P01 GM57890).
11:20 HPLC with Parallel Coulometric Array
Electrochemical and MS Detection for Redox Metabolic Profiling
Mr. Paul Gamache, Director, Applications Development, ESA, Inc.
The described technique allows pg sensitivity, 10e8 dynamic response range
and chemical structure information with fast gradient HPLC for multivariate
study of redox active small molecules. The importance of biological redox
reactions to disease, therapeutic action, metabolism and toxicity provide this
combined detection approach with the advantages of applicability to a
mechanistically targeted subset of the metabolome. Metabonomic toxicity studies,
using exploratory pattern recognition analysis of urinary metabolite profiles
obtained from animals receiving a variety of xenobiotic compounds, demonstrated
consistent differentiation from control groups and structural characterization
of potential markers of toxicity.
11:50 Panel Discussion with all Morning
Speakers
| 12:20 Luncheon Technology Workshop |
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Sponsored by |
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Brian R. Bullard, Senior Director, Computational Systems Biology,
"Computational Approaches in Metabolic Profiling" |
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Analytical Strategies
1:45 Comments by Session Chairperson
Dr. Rima Kaddurah Daouk
1:50 Evolutionary Computation for the
Interpretation of Metabolomic Data: Application to Metabolic Fingerprinting via
FT-IR and Metabolic Profiling via ESI-MS
Dr. Royston Goodacre, Department of Chemistry, UMIST (UK)
This presentation will give an overview of some of the metabolomic studies
that are currently in progress in UMIST that exploit EAs such as genetic
algorithms (GAs) or genetic programming (GP). Within this context we have been
developing Fourier transform infrared (FT-IR) spectroscopy as a high-throughput
(1 s is typical per sample), "holistic", metabolic fingerprinting
screening approach, and flow-injection, electrospray ionization, mass
spectrometry (FI-ESI-MS), as a metabolic profiling technique. The following
examples of these methods will be presented: (1) the detection of a
spore-specific chemical biomarker in bacterial spores; (2) the quantitative
detection of metabolic markers for food spoilage; and (3) discrimination of
photoperiod effects on Pharbitis nil leaf sap.
2:20 Flux Organization in Metabolic Networks
Dr. Zoltan Oltvai, Assistant Professor, Pathology, Northwestern
University
Cellular metabolism, the integrated inter-conversion of hundreds of
metabolic substrates through enzyme-catalyzed biochemical reactions, is perhaps
the most studied example of the complex intracellular web of molecular
interactions. While the topological organization of metabolic networks is
increasingly well understood, the dynamic principles governing their activities
remain largely unexplored. In this lecture, we present a flux balance-based
analysis on the conversion rate properties of the Escherichia coli metabolic
network. The results of systematic experimental verification of this framework
by global transposon mutagenesis, and the evolutionary consequences of such
organization, will also be discussed.
2:50 Characterization and Optimization of
Expert Systems that Distinguish Metabolic Serotypes
Dr. Bruce Kristal, Assistant Professor,
Dementia/Biochemistry/Neuroscience, Weill Medical College, Cornell
University/Burke Medical Research
Biochemical markers that validate (patho)physiological status may contribute
to pharmacometabolomics studies by ensuring appropriate classification of
subjects, and to drug development studies by identifying metabolites and
profiles that differ between two or more states of interest. As one stage of
identifying useful biochemical panels, we are seeking to identify a serum
profile that reflects changes in caloric intake, such as rats subject to dietary
restriction. We will present the models and the potentially general lessons for
the study of megavariate metabolomics datasets.
3:20 Poster and Exhibit Viewing, Refreshment
Break
3:50 Dietary Effects of Arachidonate-Rich Oils
and Fish Oil on Hepatic and Hippocampal Gene Expression
Dr. Alvin Berger, Manager, Cytochroma, Inc.
Microarrays are an exciting new tool for unraveling lipid metabolism.
Herein, mice were fed diets containing fish oil rich in eicosapen-taenoate and
docosahexaenoate, fungal oil rich in arachidonate, or the combination. Hepatic
and hippocampal tissue were analyzed with a combined gene
expression-lipid-profiling strategy utilizing microar-rays. In liver and
hippocampus, 329 and 356 dietary-regulated tran-scripts were respectively
identified. Hepatic genes were linked to transcription factors PPARa, HNFa, and
SREBP-1; transcription fac-tors controlling lipid metabolism. The overall
pattern of differentially regulated genes, supported with quantitative lipid
metabolomic pro-filing, suggested n6 and n3 long chain polyunsaturated fatty
acids (LC-PUFA) increased hepatic b-oxidation and gluconeogenesis, while
decreasing fatty acid synthesis. In hippocampus, LC-PUFA transcriptionally-regulated
genes were involved in appetite, learning, memory, and anxiety. Behavioral tests
(with and without CB-1 recep-tor inhibition) were performed to establish
preliminary correlations between LC-PUFA and behaviors involving pain threshold,
anxiety, depression, and aggressivity. Focused dissection of transcription
fac-tor signaling pathways combined with a more complete metabolomic profiling
are now needed to fully explain how fish oils and arachido-nate achieve their
specific health effects. Co-authors: David M Mutch, Matthew A Roberts
4:20 High-Throughput Biological Analysis of
Gene Expression Data
Dr. Bruce Hoff, Director of Analytical Sciences, BioDiscovery, Inc.
Microarray technology allows the study of an organism's metabolism in a
large scale, high throughput manner. However, this technology also produces a
bottleneck at the point at which the microarray results overwhelm the researcher
with data for tens of thousands of genes. We have developed techniques for high
throughput interpretation of gene expression data: Our approach uses
statistically rigorous algorithms to analyze the data in the context of
biological knowledge collected from a variety of public information sources,
including metabolic pathway databases. We will present the application of these
techniques to data from a lipid metabolism study, yielding novel biological
insights.
4:50 Analyzing Genome, Transcriptome, Proteome
and Metabolome Data to Accelerate the Drug Discovery Process
Dr. Adesh Kaul, GeneData
The integration of metabolomic with genomic, transcriptomic and/or proteomic
data brings together real-world end-points, i.e. actual biological events, with
genetic pre-disposition and expression changes. Relating this information to
actual phenotypic outcome provides valuable information on drug toxicity,
molecular disease signatures and gene function at several stages in the drug
discovery process. Genedata will present an in-silico solution to facilitate the
integrated analysis of diverse '-omics' data for comprehensive mode-of-toxicity
analysis of drug candidates.
5:20-6:20 Networking Reception in Exhibit Hall
Tuesday, December 9, 2003
8:15 Poster and Exhibit Viewing, Morning coffee
Application of Metabolic Profiling
9:00 Comments by Session Chairperson
Dr. Alvin Berger, Cytochroma Inc.
9:15 Metabolic Profiling in the Exploration of
Mechanisms of Toxicity: Lead in Caenorhabditis elegans
Dr. James D. Willett, Center for Biomedical Genomics and Informatics,
College of Arts and Sciences, George Mason University
We have preliminary evidence based upon lead toxicity in which tyrosine- and
tryptophan-associated pathways show fundamental changes in analytical profiles
as determined by CoulArray analysis. Of special interest is the appearance of
tyramine in the metabolic profiles of adult nematodes exposed to lead at
concentrations within the range of those suggested as safe by EPA. (Willett, et
al. 2002). An alteration in tryptophan metabolism, noted in our preliminary lead
toxicity studies, mirrors a similar response in tryptophan metabolism we find in
mouse macrophage cell lines treated with Anthrax lethal toxin. (Volchikhina S.
et. al. 2003) In the latter case we know the structure of the metabolite, which
arises via the kynurenine pathway, and is a known metal ion chelator. Examining
the correlation profiles of gene expression data with that of metabolite
profiles altered in C. elegan's response to lead should highlight processes
critical to metal ion trafficking and control within this organism. Co-Authors:
Gita Sudama and James D. Willett
9:45 Metabolomic Analysis of Motor Neuron
Diseases (MND)
Dr. Rima Kaddurah Daouk, Metabolon and Dana Farber Cancer Institute
Genetic mutations and environmental insults are believed to contribute to
the death of neurons. Specific metabolic signatures are starting to emerge for
the different subtypes of MND. Databases are established that link biochemical
changes with clinical endpoints, the chemical identification of which could
highlight disease-related biochemical and signaling events, potential
therapeutic lead molecules, and diagnostic markers for the diseases.
10:15 Comprehensive analysis of E. coli
Metabolome
Dr. Masaru Tomita, Institute for Advanced Biosciences, Keio University
(Japan)
Abstract Unavailable at Time of Printing
Attempts are being made to analyze and list up all
intracellular metabolites of E.coli. For systematic and high-throughput
detection of metabolites ranged from 70 to 1,000 molecular weights, we use CE/MS
for charged species and LC/MS for neutral molecules. Unknown peaks are
further investigated by CE/TOF-MS, CE/MS/MS, LC/TOF-MS and LC/MS/MS to identify
their represent-ing metabolites. Bioinformatics algorithms are then applied to
con-nect these metabolites into pathways.
10:45 Poster and Exhibit Viewing, Refreshment
Break
11:15 Metabolite Profiling: A Powerful
Approach to Functional Biology
Dr. Richard Trethewey, Chief Scientific Officer, Metanomics GmbH & Co
KGaA
Metanomics has implemented an integrated, high-throughput, metabolite
profiling platform encompassing automatic extraction technologies and chemical
analysis with GC-MS and LC-MS. Examples of the successful application of this
platform to the discovery of high value lead genes in plant functional genomics
will be covered. The wider potential of metabolite profiling will also be
demonstrated, with examples drawn from metabolic engineering and pharmaceutical
studies, and the power of combining metabolite profiling data with literature,
annotation, expression and phenotypic data will be illustrated.
11:45 GenMAPP and MAPPFinder: Tools for the
Organization, Display, Analysis, and Exchange of Pathway Information
Dr. Kam Dahlquist, Professor, Vassar
Abstract Unavailable at Time of Posting
12:15 Panel Discussion with All Morning Speakers
12:30 Lunch on your own
Pharmaceutical Applications
2:00 Comments by Session Chairperson
Dr. Alvin Berger, Cytochroma Inc.
2:05 Gene to Cell to System
Dr. Alan Higgins, Senior Director, Investigative Medicine,
Paradigm Genetics, Inc.
Routine assays for prediction of toxicity often result in false positive and
false negative findings. In the case of liver toxicants, tests used to evaluate
toxicity in vivo assess hepatocyte integrity rather than liver function.
Approaches such as gene expression profiling are non-specific, expensive, and
invasive, and may generate only limited information on the precise mechanism(s)
of drug action. Metabolic profiling is an important discipline focused on the
comprehensive analysis of the low molecular weight biochemicals present in
cells, tissues and biofluids. The ability to combine metabolic profiles with
other data streams, including histopathology and pathway data, can provide
additional information beyond a simple injury signal, and lays the foundation
for a mechanism-based, minimally invasive approach to predicting long-term drug
safety and human outcomes. This presentation will focus on the use of suites of
metabolomic markers to assess liver toxicity from gene to cell to system, and
how this data can be combined with other data streams in a systems biology
approach to understand mechanisms underlying toxicity and disease.
2:35 Metabolite Profiling with LC-MS: A Novel
Method that Combines Screening and Target Analysis
Dr. Tilmann Walk, Bioanalytics, Metanomics GmbH & Co KGaA
Metanomics has developed a novel LC-MS method that enables both a non-biased
screening of complex matrices combined with a focused and sensitive target
analysis using triple quad technology. This method enables the routine
coverage of several hundred analytes in a single analysis and the development of
software for automatic quality control and data validation has enabled the
method to be implemented in high throughput (1000 chromatograms per day with 10
systems). In this presentation the approach being taken will be illustrated with
examples of metabolic profiling studies in plant and pharmaceutical research.
3:05 Probing Biofluids Using Mass Spectrometry
and Metabonomics
Dr. John Shockcor, Metabometrix Ltd.
Metabonomics is a science which has the potential to redefine the selection
of drug candidates, and understand clinical and preclinical mechanisms, clinical
trial design and diagnostic development, through the application of advanced
data analysis techniques to metabolite profiles of biofluids. Expertly applied
metabonomics can extract the critical information from complex spectral data
which reveals the biochemistry of toxicity, disease and drug intervention. In
this talk we describe the application of mass spectrometry to metabonomics, and
will present examples illustrating its utility in probing mechanisms of toxicity
and disease diagnosis. We will also show how NMR spectroscopic and mass spectral
data complement each other, providing a more complete picture of important
biochemical processes. Co-Authors: Andrew Nicholls, Henrik Antti, Jose
Castro-Perez, Hilary Major, and Rob Plumb
3:35 Poster and Exhibit Viewing, Refreshment
Break
4:05 Lipomic Profiling in Drug Discovery and
Development
Dr. Steven M. Watkins, President & Chief Scientific Officer, Lipomics
Technologies, Inc.
Lipomics employs a quantitative assay (TrueMass®) that measures
approximately 500 lipid metabolites from tissues and fluids, and a proprietary
battery of steady-state metabolic flux equations for interpreting lipid profile
data. Lipomics is using these technologies to develop a large quantitative
database of lipid profiles in human clinical populations, and to develop an
improved understanding of lipid metabolism and its relationship to metabolic
health, drug efficacy, drug safety and nutrition. This presentation will provide
examples of the use of lipomic profiling to improve knowledge of lipid
metabolism in drug discovery, drug development, functional genomic and clinical
applications.
4:35 Metabolic Profiling: Value Added Technique or Distraction? Case Studies
in Pharma
Dr. John Haselden, Head, Metabonomics Group, GlaxoSmithKline (UK)
Summary unavailable at time of posting
5:05 Panel Discussion with all Afternoon
Speakers
5:15 Close of Conference
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