Metabolomics for Bioscience Research

The significant global investment in genomic and proteomic tools for biochemical sciences has led to a rapid increase in our understanding of the genetic basis of cellular function and the influence of genetic changes on the proteome. However, downstream effects on metabolism remain significantly under-investigated but hugely important as they can manifest in changes to energy production, cell maintenance, proliferation and signalling. It is also in the metabolome that a direct interface with the external environment takes place. Metabolomics aims to provide comprehensive analysis of the entire small molecule component of biological samples from cells to whole organisms. Comprehensive metabolomics can be used as a discovery tool to assess the impact of upstream alterations to genetic and proteomic expression as well as the effects of environmental inputs on cellular metabolism.
In Oxford Chemistry we have recently pioneered metabolomics of central energy metabolism which uses ion-exchange chromatography-mass spectrometry. Although very effective it can only be used for physiologically ionic and highly polar metabolites and does not give wide metabolome coverage. Furthermore it is funded for medical and clinical sciences and very heavily used for this. Researchers in the biosciences at Oxford desperately need a dedicated metabolomics platform to focus on fundamental biology, plant science and physiology. For example in the applicant's research in plant sciences metabolic profiling will benefit the investigation of plant-pathogen molecular relationships and normal functioning symbiotic relationships including nitrogen fixing bacteria interactions. Also studying the behaviour and functioning of plant metabolic networks to increase crop yield and resistance to disease. In physiology metabolomics will be used to study ketone metabolism, dietary performance response, hormone secretion by the gut and metabolism of infection. In fundamental biology and chemical biology metabolomics will play a key role in understanding mechanisms of sucrose signalling, algal responses to hypoxia, the interaction of redox balance and genetic studies interpreting the effects of DNA modifications on cellular pathway function and on artificial DNA synthesis to understand nucleic acid chemistry in vivo, develop therapeutic interventions and understand epigenetic regulation.

We propose acquisition of a state-of-the-art Ion Mobility Mass Spectrometry system coupled to Ultra-Performance Liquid Chromatography (LC-IMS-MS/MS). This platform has excellent metabolite coverage of lower polarity metabolites including, importantly, lipids and plant secondary metabolites, using reversed phase chromatography. Ion-mobility capabilities will enhance metabolome coverage and increase confidence in compound identifications. The instrument will therefore provide an exceptional platform for metabolome-wide profiling. Furthermore this will complement other non-metabolomics capabilities dedicated to research in the biosciences enabling systems level analyses from genome expression to metabolome coverage. The proposed instrument does not overlap, but instead will be synergistic with existing capabilities enabling current and future BBSRC researchers from across the biosciences to move forward the frontiers of knowledge in systems biology, chemical biology, and the physiological and plant sciences.
The new instrument will be integrated into the existing mass spectrometry laboratories (MS-SRF) in the Department of Chemistry in Oxford. It will be multi-user, enabling BBSRC-funded research groups in Oxford and the UK, to have dedicated access. The instrument will support research projects spanning a range of BBSRC strategic research priority areas, and will become an integrated piece of equipment in the Interdisciplinary Biosciences Doctoral Training Programme, making it available to researchers at other sites including Oxford Brookes University and the Diamond Light Source.

A major current challenge in biochemical science is to understand the purpose and relevance of genes, their products (both proteins and nucleic acids) and the impact of these on the cell phenotype (the metabolome). The phenotype is also affected by interactions with the downstream external environment of the cell/organism. Understanding the inter-relationships between biochemical systems within cells and their environment in context will lead ultimately to improving our ability to understand the health implications of behaviour in humans, plants and animals, manipulate genetics and metabolism effectively, and provide strategies for improving crop health, resistance to pathogens and the effects of environmental change of organisms.

We will address these challenges by capitalizing on recent technical developments in LC-MS/MS for dedicated targeted and untargeted metabolite profiling. We propose to purchase an ion-mobility high resolution time of flight tandem mass spectrometer coupled with ultra-performance liquid chromatography which will provide highly selective, sensitive and robust analytical capabilities. This will become the first dedicated instrument for metabolomics focused on bioscience research in Oxford but will complement an existing ion-chromatography-MS system used for medical and clinical metabolomics which covers exclusively physiologically ionic and very highly polar metabolites only. The coverage the two instruments combined will provide is likely to be unique in the UK and an exceptional asset to enable state of the art capabilities for bioscience research.

The proposed equipment will revolutionize our ability to perform untargeted and untargeted metabolic profiling across the diverse spectrum of BBSRC research taking place in Oxford. In doing so it will help fit together what in some ways is the last piece of the biological puzzle; to determine how genes, proteins and environment contribute to cellular function in context.

This new equipment represents a cutting edge solution to address an important problem, namely understanding how genes and proteins and the environment impact on metabolism. The metabolomics platform for the biosciences will complement existing MS equipment for proteomics, structural and chemical biology, and high throughput ligand screening. It will also leverage an existing highly specific capability for physiologically ionic untargeted metabolomics. This will have significant impact on the applicant's active research and other BBSRC funded research in Oxford and beyond. The equipment will be truly multi-user, enabling research across the BBSRC remit, and place Oxford at the forefront of international biological mass spectrometry (MS). We are committed to ensuring that the publicly funded equipment will play an important role in contributing to translating fundamental research into positive benefit for the health and economic prosperity of UK society.

Basic Science:
The research enabled by untargeted and targeted metabolomics is likely to have significant downstream impact on the community of scientists working on understanding the function of genes and the structure and function of proteins particularly in biological context. The research areas of the many users of the proposed equipment span BBSRC Strategic Research Priorities (see Case for Support). Based on the track-record of the applicants, the research enabled will be published in high-quality journals, presented at international conferences, and if appropriate, filed as patent applications or used to form spin out companies, with which Oxford has an outstanding track record (e.g. £16.9m for OxStem and its subsidiaries: http://www.oxstem.co.uk/).

Industry:
The pharmaceutical, agrochemical, and biotechnology industries are vital to the UK economy, employing >250,000 people and generating billions of pounds of tax-revenue. The application of new metabolomics methods is enabling a new understanding of how environmental changes, pathologies, interactions of organisms and individual compounds affect biological systems and in doing so are providing information relevant to the underpinning of much of the research in these industries which do not generally have dedicated infrastructure for comprehensive, untargeted metabolomics for example. We will actively engage these companies to share our methodologies. We have extensive links with industry for collaborative research including with GSK, Syngenta and Rothamsted Research.

Training:
The multi-user equipment will facilitate training directly of >80 PhD students per year in biological MS technologies as part of their introductory year on BBSRC-funded DTC and DTP PhDs (http://www.biodtp.ox.ac.uk/) as well as the EPSRC-funded Synthesis for Biology and Medicine CDT (http://www.oxfordsynthesiscdt.ox.ac.uk/). In addition, >300 full-time researchers in Oxford will have access to metabolomics and its capability, with the opportunity to be trained in the technique and the analysis of the ensuing data. Similarly, visitors from laboratories outside Oxford will potentially benefit from exposure to these techniques.

General public and related outreach:
The University has established routes for engaging the general public with our research. Aside from the engagement activities on-going in the labs of all the users, we also regularly host summer students, give tours of the MS facility (including demonstrations) to school children; and invite prospective University applicants to see the labs during Open Days, so they can experience a cutting-edge research environment. Recent outreach activities include museum exhibitions focusing on BBSRC-related work including 'Biosense' and 'Back from the Dead', the first focusing on how basic BBSRC science led to the discovery of a family of oxygen sensors and the latter on antibiotic discovery and resistance (see http://www.mhs.ox.ac.uk/backfromthedead/).