Institute for Health and Consumer Protection
Acronym: Systems Toxicology
Role of the Systems Toxicology Action
The Systems Toxicology Action will deploy a range of competences in high-throughput screening, "omics" and computational toxicology to support EU policies on health and consumer protection. Particular focus will be placed on the development, assessment and application of methods for assessing the adverse effects of chemicals in substances, food and consumer products. This will include the development and evaluation of Integrated Testing Strategies that provide the information needed for hazard assessments. Efforts will also focus on the development and dissemination of freely accessible databases and software tools. The Action will support customer DGs and other organisations via the horizontal policy support actions of the IHCP and also contribute to competitive research projects.
In 2009, the Action activities will be centered around four competences:
The following sections summarise the activities within each competence area.
High-throughput screening (HTS):
Automation of bioassays offers a number of significant advantages over manual implementation, including a high level of precision and throughput. Moreover, consideration of automation aspects during the development and validation of an in vitro assay can significantly aid in the eventual uptake of the test by industry. The role of HTS within the Unit/IHCP will be threefold, namely, to support the optimisation and standardisation of robust and informative cell-based and biochemical assays, to generate high quality in vitro data sets using selected libraries of reference substances, and to demonstrate how HTS can be combined with computational toxicology and "omics" approaches for targeted safety assessment of chemicals and nanomaterials.
HTS, based on the automation of in vitro biological/biochemical assays, is gaining wide acceptance in modern toxicology, as reflected in the multiagency ToxCast and Tox21 programmes being undertaken in the USA. The aim is to combine the benefits demonstrated in pharmaceutical discovery in terms of throughput and time/cost saving with the rigour required for toxicity testing. Some recent initiatives are also looking to HTS as a key element in safety assessment of nanomaterials. Quantitative-HTS, initiated by the NIH Chemical Genomics Center (NCGC) and now implemented in the HTS facility of IHCP, is an excellent example of how to adapt HTS approaches to satisfy the demands of toxicity testing. This approach is very reliable and produces significantly lower false-positive and false-negative rates than the traditional HTS methods, but still offers impressive throughput. The state-of-the-art facility of the IHCP-JRC consists of two comprehensive robotic platforms supported by ample cell culturing and compound management (repository) laboratories. A pharma-type data management and analysis system is also linked to the facility to ensure reliable treatment and traceability of test data. In support of the main HTS systems, research effort is also being invested in applying and assessing the added value of evolving assay technologies such as high content functional imaging for cell analysis, micro-electrode array (MEA) platforms for electrophysiological measurements, and nanobiotechnologies for controlling cell differentiation
Genomics, proteomics, metabolomics and metabonomics:
Genomics is a science that attempts to describe a living organism in terms of the sequence of its genome. Genomics uses the techniques of molecular biology and bioinformatics to analyse the sequences attributed to structural genes, regulatory sequences, and even non-coding sequences. Proteomics focuses on identifying when and where proteins are expressed in a cell so as to establish their physiological roles in an organism.
Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically, the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological organism, which are the end products of its gene expression. Metabonomics is defined as "the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification". This approach is increasingly used in toxicology, disease diagnosis and a number of other fields including nutrition. One of the challenges of systems toxicology, and more generally systems biology, is to integrate proteomic, transcriptomic and metabolomic information to give a more complete picture of living organisms.
Metabolomics and metabonomics provide an overview of the metabolic status and global biochemical events associated with a cellular or biological system. They can accurately and comprehensively depict both the steady-state physiological state of a cell or organism and of their dynamic responses to genetic, abiotic and biotic environmental modulation. An increasing focus in metabo(l/n)omics research is now evident in academia, industry and government (e.g. metabolomics is part of the vision of the US National Institutes of Health [NIH] road map initiative, c.g., Zerhouni E (2003). Science 302, 63-64 & 72).
Nuclear Magnetic Resonance (NMR) and high-resolution Mass Spectrometry (MS) are the two key complementary analytical techniques that are used to record metabolic fingerprinting of cultured cell extracts and/or human or animal biofluids. NMR and MS spectroscopic profiles are collected in databases together with the metadata related to chemical, biological or physical exposure and/or health status of subjects. The spectroscopic data is analysed by chemometrics (see below) to assess the metabolic response to exposure or toxic effects of chemicals.
The Computational Toxicology project promotes the development, assessment, acceptance and implementation of computer-based estimation methods suitable for the regulatory assessment of chemicals. This includes methods for predicting the effects of chemicals on human health and the environment, as well as their distribution and fate within the environment and biological organisms. The work is based on the development and use of chemical information systems, toxicoinformatics tools, and theoretical and mechanistic models based on a range of methodologies, including statistical, mathematical and molecular modelling approaches, as well as environmental fate models. This includes the development of chemical categories and quantitative-structure-activity relationships, as well as investigations into their applicability in risk assessment, e.g. in the setting of Environmental Quality Standards (EQS) and in the derivation of Environmental and Toxicological Thresholds of Concern.. Emphasis is placed on the development of publicly available and web-based computational tools and their application in the assessment of chemicals under various regulatory frameworks.
Information Systems, Chemometrics and Statistics:
A comprehensive information system on the availability of alternative methods is key to the success of the JRC Action Alternative Methods and ECVAM. A dedicated database service provides information e.g. on evaluated data sheets on various aspects of alternatives as well details on validation studies.
Chemometrics is the application of mathematical or statistical methods to chemical data. Chemometrics is essential for the processing of the large analytical data generated by MS and NMR spectroscopy with the metabolomics approach. Supervised and unsupervised multivariate analysis methods are used to explore the analytical data and to help identify biomarkers and metabolic patterns induced by exposure to chemicals.
This competence area applies statistical methods to support: a) the design and analysis of test method validation studies; b) the optimal design of Integrated Testing Strategies, and c) the statistical analysis of experimental (e.g. spectroscopic) data generated in IHCP laboratories.
Activities of Systems Toxicology Action in 2009:
In 2009, the Systems Toxicology Action will build up capacity in the field, will identify customer requirements and will establish a network of external collaborators, with a view to developing a multi-annual work programme for 2010 and beyond. Given the wide scope of the field, and the large number of other organisations already engaged in the broader subject of systems biology, it will be important to position the JRC in a way that meets customer requirements and adds value to external activities. The work will also focus on the design, assessment and application of Integrated Testing Strategies (ITS) in support of chemical hazard assessment.