Bioresearch Online Interview With John Ryals, Metabolon, Inc.

John Ryals, Ph.D., Board Member, President and Chief Executive Officer, received a Ph. D. in Molecular Biology from the University of Texas at Dallas. Prior to joining Metabolon, Dr. Ryals was CEO, President and Founder of Paradigm Genetics, Inc. There, he raised over $100 million in equity financing, including an Initial Public Offering in 2000 and a follow on offering in 2001 and closed on R&D partnerships valued at over $200 million. Dr. Ryals has 20 years of experience in the biotechnology industry including senior research positions at Novartis and Ciba-Geigy and currently serves on the Board of North Carolina State University College of Physical and Mathematical Sciences.

1) Describe metabolomics and explain how it is used to discover biomarkers.

Metabolomics is the study of the small molecule biochemistry of an organism. The goal of metabolomics is to understand the metabolic state of a subject by extracting, identifying, and quantifying all of the small molecule compounds (e.g. metabolites) in a biological sample. Since it is based upon biochemistry and provides a measurement of the biological status of an organism, metabolomics provides a powerful new technology for biomarker discovery. Unlike other "omics" technologies, metabolomics provides a biochemical signature that takes into account not only genetics, but also the effects of lifestyle, diet, and environment on the health status of an individual. Metabolic biomarkers of disease and/or drug-induced changes can be discovered from studies designed to identify differences between groups of individuals. The soundness of this approach is supported by the fact that biochemicals have been used for diagnostic purposes for hundreds of years and are routinely used in modern medicine (e.g. glucose for diabetes, cholesterol for heart disease). In fact, biochemistry itself is an established field of science that allows the physiological impact of observed changes in metabolites uncovered by metabolomics analyses to be understood.

The primary objective of metabolomics for biomarker discovery is to characterize metabolite differences between altered, stressed or otherwise abnormal physiological states. Studies must be well-designed with sufficient statistical power. Sample collection protocols must be carefully designed and consistently followed. Metabolites that are present at different levels in the states are candidate biomarkers for such states. Once the candidate metabolite biomarkers are validated, biochemical assays can be developed that are specific for the biomarker analytes. These targeted assays are then useful for diagnosis in a clinical setting, as is typically done for many disease biomarkers such as glucose for diabetes.

2) There are a number of organizations that provided metabolomic services. What is Metabolon's approach and what advantages does it offer?

Metabolon's compound-centric approach to metabolomics is unique and provides a valuable point of differentiation in the field of metabolomics solution providers. At Metabolon, signals from our mass spectrometers, both LC/MS and GC/MS, are analyzed by our proprietary informatics system. In this environment, peaks are automatically isolated and referenced to our library of approximately 1,000 known compounds. All subsequent analyses are performed these compounds and, compared to analyses performed on mass spec or NMR output, this approach offers significant advantages to our clients. Metabolon's compound-centric approach provides interpretable results for disease diagnosis, disease progression, drug efficacy, or drug safety by providing:

• Specific biomarkers
  
• Evaluation of the altered biochemical pathways
  
• Determination of the biological impact and risk associated with these changes

In addition to the advantages of a compound-centric approach, scientists at Metabolon have optimized the workflow for sample preparation and sample processing. Over approximately the past five years, we have taken a Quality Assurance approach to improving and validating each phase of these processes.

Sample Preparation: The biological samples used in Metabolon's studies can be biological fluids (plasma, urine, CSF), tissues, or cells. Metabolon's methodology for extracting metabolites from proteins has been established and has demonstrated to provide low variance while simultaneously maximizing the extraction of diverse compounds.

Sample Processing: To quantitate all of the small molecules in the extracts, Metabolon uses parallel chromatography and mass spectrometry instruments. Specifically, each sample is analyzed simultaneously with LC/MS and GC/MS so that all charged compounds or ions can be observed. Since ion suppression or ionization efficiency can be inefficient for certain molecules on one of these systems, this dual-platform approach provides an optimized solution for measuring the majority of compounds that can exist in any biological sample.

3) What are the differences between metabolomics and genomics and proteomics? Are there any advantages?

Since changes in metabolites are the ultimate result of altered physiological states, metabolomics falls within the central dogma of biology: DNA-to-RNA; RNA-to-Protein; and Protein-to-metabolite. However, while the genome, transcriptome and proteome are estimated to be quite large, the metabolome is relatively small by comparison. For instance, while there are estimated to be 25,000 genes, 100,000 transcripts, and more than one million proteins in humans, our research shows there are only approximately 2,400 metabolites. Rather than having to perform analyses to identify trends in large data sets, this small number of metabolites allows for us to perform standard statistical analyses which offer clear and definitive results. Further, these smaller data sets significantly decrease chances of false discovery so that, in the end, scientists can use the results to make robust and actionable decisions.

4) How do you see metabolomics evolving in the next few years? Are there any additional benefits that may increase the acceptance of this emerging technology?

Today, the acceptance of metabolomics for biomarker discovery, drug safety testing, and evaluation of drug efficacy is rapidly growing. We expect this growth to continue and, ultimately, establishing metabolomics as a key technology in the drug discovery and development infrastructure. The justification for this prediction is based on the client feedback on the results of our studies and, specifically, how this offered clear results and the ability to make crisp and actionable decisions.

Most importantly, metabolomics offers a unique value for drug and diagnostic development because these biochemical-based results can be more predictably translated across organisms. While each organism has a unique genome resulting in a unique transcriptome and proteome, small biochemical molecules themselves are highly conserved across species. Clearly, most organisms use the same amino acids to make proteins and essential processes such as glycolysis and lipid biosynthesis are very similar if not identical. The ability to achieve clear results that are translatable across species and even between eukaryotes and prokaryotes can put metabolomics in a position to significantly improve drug and diagnostic discovery and development.