I asked Dr. Warwick (Rick) Dunn, an expert in clinical metabolomics, if he could share his knowledge and experience of metabolomics with us all.
Rick is a Lecturer in Metabolomics and the Director of Mass Spectrometry in the £8M Phenome Centre-Birmingham at the University of Birmingham in the UK. Rick trained as an analytical chemist and has been applying metabolomics to study microbes, plants and mammals for 15 years.
Why are metabolites important in human health, aging and the development and progression of diseases?
Metabolites are key biochemicals in all living systems. They are central to metabolic activities in the cell, including the breakdown of food into metabolites (catabolism) and the synthesis of other metabolites and biochemicals, including proteins, RNA and DNA (anabolism). However, metabolites are also important in the regulation of biochemical processes, signaling processes, and in the construction of cellular structures. The metabolic network is dynamic and changes occur rapidly; metabolism is the Formula One of biochemical processes! In a study investigating metabolic changes following a ‘planned’ heart attack, we have shown changes in multiple metabolic pathways in blood one minute following the start of the event. Studying metabolites provides a sensitive and dynamic marker of the genotype-environment interaction, the phenotype, at the molecular level. Many groups define these studies as metabolic phenotyping or metabolomics.
Why are discovery studies still important in metabolomics applications?
After more than 100 years of biochemistry discovery, there are still many metabolites and metabolic pathways that are not fully characterized or described in online databases. For example, metabolism of the different organisms in the human gut has a large impact on human health, disease and ageing, yet in comparison to human metabolism much less is known about metabolism in these organisms. Many metabolites we can detect in humans are not derived from human metabolism but are taken in from the environment in food, liquids, gut microflora metabolic products and medications. Furthermore, our understanding of metabolism in human health and diseases is not thoroughly characterized, so there are still many discoveries to make. For example, in studies I perform, aromatic amino acid metabolism appears to be important in ischemia and hypoxia, but little is known on this topic. Until ten years ago, little was known about the important role branched chain amino acids have in the development of insulin resistance and diabetes. Today there are over 500 papers published on this topic and multiple translational studies are being performed.
Why are discovery and validation steps essential for new translational successes?
To study the role of metabolites we need to investigate the system as a whole, in a discovery-based approach. Here we apply complementary approaches, including liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and NMR spectroscopy to investigate a diverse range of metabolic pathways. In many cases this is viewed as a fishing trip, but in my studies these are successful fishing trips, when studies are designed robustly, that provide novel insights in to mechanism and identify putative biomarkers to be applied in stratified medicine. However, metabolomics is only the first step, it constructs a hypothesis based on a small set of metabolites, which needs to be validated. Further biological or clinical studies have to be applied to validate the hypothesis constructed.
Why is mass spectrometry an important tool to apply in metabolomics studies?
Mass spectrometry provides many strengths to enhance metabolomics studies or targeted assays. High mass resolution allows the separate detection of metabolites with similar monoisotopic masses, and with high mass accuracy measurements, we can accurately determine mass and molecular formula. When integrated with ultra high performance liquid chromatography, powerful spatial separations provide the detection of thousands of metabolites from diverse sample types, and when different and complementary sample extraction and UHPLC chemistries are used this extends the coverage of the metabolome. The acquisition of fragmentation mass spectra (MS/MS or higher levels of MSn) provides a route to chemical identification of metabolites. Mass spectrometry also provides multiple advantages in targeted assays, including high levels of sensitivity and specificity in well-developed assays; LC-QQQ-MS is the gold standard for targeted assays in many regulated industries, including pharma.
What are the current bottlenecks in metabolomic studies?
Metabolomics is a young scientific discipline. The first use of the term metabolomics was in the year 2000. The discipline has grown rapidly in these 15 years, driven by advances in analytical technologies (e.g. the Orbitrap mass analyser and the UPLC system developed by Waters) and computational tools. However, there are a number of bottlenecks that are currently unresolved, including:
Collection of adequate sample numbers in clinical studies where hundreds to thousands of samples are required for a valid study
Chemical annotation or identification of metabolites detected in metabolomics studies; in many groups globally only 50% of detected metabolites are identified
Standardization and public availability of data; MetaboLights and the Metabolomics Workbench are providing the capability to make data available, but many groups still do not use this resource
Is training an important area for development in the field of metabolomics?
Metabolomics is a rapidly growing scientific field and the number of new researchers applying metabolomics is increasing. However, there are only a small number of centres that provide training, and to support the growth of metabolomics, we have constructed the Birmingham Metabolomics Training Centre to provide face-to-face and online courses.
How are you applying metabolomics in clinical research in Birmingham?
I apply metabolomics and targeted assays in multiple research areas, including endocrinology and metabolism research, musculoskeletal health, arthritis, trauma, cancer, and exercise. Our studies are focused on two goals:
(1) To understand molecular mechanisms associated with how we age and how a disease starts and progresses to identify nutritional, exercise or pharmaceutical interventions
(2) To identify metabolic biomarkers to apply in stratified medicine.
Currently, individual human beings are viewed as equal, with the assumption that all people react in the same way to their genotypes and environment. This is not true. The population can respond differently, and being able to identify which patients will respond (or not respond) to a specific treatment can impact, for example, on survival rates in cancer. So by being able to stratify the population into groups upon which appropriate treatments will be successful or in which different levels of screening for a disease are applied can only benefit the human population and save money for healthcare systems. For example, we are studying metabolic changes following a burn trauma and have shown longitudinal changes in metabolism that could be detrimental to recovery, but can be improved through nutritional interventions. In the same study we have identified putative biomarkers (which we are now working to validate) that predict patients who are at greater risk of sepsis during the first ten days following trauma, and these patients can then receive different clinical management than patients without sepsis infection risk.
In a recent webinar, Dr. Rick Dunn discussed how and why metabolomics is applied in clinical research, how MS is applied to acquire robust data on thousands of metabolites in small and large-scale studies of the human population, and talked at length about the first example of large-scale untargeted metabolic profiling applying UHPLC-MS, the HUSERMET project.
For further information on biomedical and clinical research and training programmes at the University of Birmingham, visit the resources below: