Developing the Ecotoxicological - Predictive - Information - Connectivity Map (EPIC-map)

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

A fundamental challenge within the environmental sciences is to establish the relationship between exposure to a chemical stressor, its molecular effect and the resulting adverse outcome. Particularly in risk assessment it is desired to identify or predict the adverse outcome before its manifestation. To this effect, computational (predictive) biology aims at developing techniques and methodologies to identify molecular pathways and physiological endpoints that can be directly linked to the adverse outcome. The Environmental Protection Agency (US EPA) following a White House Mandate in 2003 has placed computational predictive ecotoxicology at the centre of their R&D strategy and since then has been heavily investing into this technology. In the UK, the NERC has also recognised the importance of a computational approach to integrating multi-level complex datasets by establishing the Environmental Omics Synthesis (EOS) initiative and by including Systems Biology as one of the core research priorities.
An essential part of the these programs is the adverse outcome pathway (AOP) framework, developed by G. Ankley et al at the US EPA.This was designed to link available knowledge on key events in a logical chain of events, from the molecular initiating event to organism molecular and physiology response and leading up to and including the adverse outcome. The resulting pathways could then be interrogated and used to support risk assessment and environmental monitoring. As the number of AOPs increase more robust predictions can be made on the effect a novel compound may have on a given organism.
At the core of the AOPs is the reconstruction of molecular pathways leading to adverse outcomes. This requires extensive and highly complex datasets allowing for an unbiased approach. The underpinning computational tools required to develop an AOP from such data should therefore be able to
1) reconstruct the underlying regulatory network,
2) link the molecular response to the adverse outcome,
3) link structural features of compounds to molecular response, and
4) provide an interpretive output for AOP and hypothesis generation.
Finally, the results developed from a set of known compounds forms the basis for deriving predictions on the potential molecular effect of novel chemicals on a given organism.
This project proposal addresses this important need by developing the necessary computational framework in collaboration with the US EPA which directly integrates with their FY2015-17 research plan to develop and validate computational (eco)toxicology techniques to integrate and eventually transition away from traditional assays. To achieve its goals the project will start by integrating various publicly available databases with a purpose built standardized dataset of 200 compounds into a single database. Links between the genes and compounds will form the basis of the networking approach, while the standardized dataset will be used for identification purposes and predictive modelling. To interrogate the database the project will utilize a number of tools currently used by many computational biologists and in addition incorporate a set of predictive modelling approaches. This will allow any bench user to identify compounds linked to their molecular response, gene-gene-chemical-adverse outcome networks for AOP development and hypothetical prediction of molecular effect of yet untested compounds via chemical structure. This will provide a basis for risk assessors such as the US EPA, UK Environmental Agency or European Commission Joint Research Center and many other high level and academic organisations to develop hypotheses on the potential risk and effects a chemical may have on an organism.

Planned Impact

The primary objective of this project is to develop a simple to use web-service that allows any bench user to identify and compare their observed molecular response to a database containing an environmentally-relevant standardized dataset and an integration of a number of databases to provide hypotheses on gene-gene-compound interactions and potential adverse outcomes. As such this project has great value in environmental monitoring, risk assessment and identification of adverse outcome pathways (AOPs).

My Fellowship proposal is formally supported by a number of advisory and regulatory bodies within the UK (Cefas - Centre for Environmental, Fisheries and Aquaculture Science - see letter of support (LoS) Ioanna Katsiadaki) and US EPA (US Environmental Protection Agency - see LoS Rong-Lin Wang), as well as other leading environmental institutes US ERDC (US Engineer Research and Development Center, Corps of Engineers, see LoS Ed Perkins), NIVA (Norwegian Institute for Water Research, see LoS Knut-Erik Tollefsen), Nanjing University (see LoS Xiaowei Zhang), IGBB (Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University - see LoS Natalia Reyero Vinas), University of Florida (see LoS Nancy Denslow) and the Consortium for Environmental Omics and Technology (see LoS John Colbourne) to develop and advance these techniques in the environmental sciences. Upon successful validation of the tool through the use of data developed at the supporting institutes, access to the wider scientific community will be provided. Additional stakeholders from the following list may also be highly interested in the success of this project:
1. Regulatory and monitoring bodies (US EPA, OECD, UK Environment Agency, Cefas, Defra, Public Health England, European commission Joint Research Centre, ECVAM, Umweltbundesamt (UBA)
2. Industry such as Unilever, AstraZeneca, UK Water and Sewerage Companies, European Chemical Council (CEFIC), Waternet
3. Academia, Groups involved in Ecotoxicology, AOP development and monitoring, NC3Rs
4. General Public
The EPIC-map will provide the international community with the computational tools and hypothesis-generating abilities of state-of-the-art computational biology approaches driving the identification of AOPs and compounds in the environment. In addition, animal usage could be drastically reduced through the use of the zFET. To facilitate the update of this platform, and its incorporation into future risk assessment and environmental monitoring protocols, I will assemble an expert steering panel from international stakeholders and collaborators to this Fellowship. They will consult periodically on a range of issues focused on its relevance to their sector; the selection of compounds, the development of the EPIC web presence, delivery of AOP compliant outputs, coordination of standards for lab protocols and informatics processing, and the need for validation to meet the needs of regulatory authorities etc. Due to the time and distance limitations, this discussion will typically occur via videoconferencing (AccessGrid/Skype). Part of the impact workshop in Year 3, which is described in the next section, will be a key advisory meeting of representatives of stakeholders listed above to focus on the means of seeking regulatory approval and further developmental direction.
 
Title EPIC-map website 
Description The EPIC-db is the heart of the EPIC-map and is developed as part of the grant. It houses the database and web interface to add data and interact with the data that is available. It is still under construction but is used by the group to test and further develop the tool 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? No  
Impact None yet 
URL http://epic.liverpool.ac.uk
 
Title EPIC-db 
Description The EPIC-db stores and collects data from experiments undertaken during the award. It allows for storage, analysis and visualisation of experimental results. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact The EPIC-db allows for rapid analysis and will be made available to the wider scientific community after extensive testing. It is currently in testing with collaborators at Cefas. 
 
Description AstraZeneca EPIC-map Support 
Organisation AstraZeneca
Country United Kingdom 
Sector Private 
PI Contribution The EPIC-map will strive to expand the underlying dataset to include multiple concentrations to allow for a more quantitative approach to AOPs which is one of the main interests for AstraZeneca.
Collaborator Contribution AstraZeneca is providing knowledge and experience in the experimental design process and the selection of compounds. The partners have extensive collaborations and experience in the zebrafish embryo test and are proving to be great resource.
Impact The only outcome that has resulted from this collaboration so far is the expanded and improved experimental design for the development of the underlying dataset to the EPIC map. Within the improved design, a specific Zebrafish strain was identified for which a lot of behavioural data is known and AstraZeneca will provide access to as much as possible.
Start Year 2015
 
Description Cefas EPIC-map Support 
Organisation Centre For Environment, Fisheries And Aquaculture Science
Country United Kingdom 
Sector Public 
PI Contribution There will be yearly seminars and additional collaborations with offshoots of Cefas to support the use of computational biology in risk assessment and general science.
Collaborator Contribution The partner is providing animal units and ecotoxicological facilities as well as access to microscopy units specifically designed for these type of analyses. The partner will also engage directly in the selection of compounds and the experimental design - particularly the dosing of the zebrafish eggs.
Impact The outcomes so far include a submission for an industry CASE studentship to Cefas, which sadly wasn't funded. There will be additional papers from the collaboration which will strengthen the use of computational biology in ecotoxicology.
Start Year 2013
 
Description Nimbios 
Organisation Bowling Green State University
Country United States 
Sector Academic/University 
PI Contribution Provide knowledge and techniques for molecular analyses of Daphnia magna. Train PostDoc and Collaborator in RNA extraction and subsequent analysis of data.
Collaborator Contribution As part of the ongoing collaboration, we provide knowledge and expertise around ecotoxicology to each other.
Impact An NSF Eager Grant application in the US. Further publications on the way and more data generation and analysis.
Start Year 2018
 
Description Nimbios 
Organisation Michigan State University
Country United States 
Sector Academic/University 
PI Contribution Provide knowledge and techniques for molecular analyses of Daphnia magna. Train PostDoc and Collaborator in RNA extraction and subsequent analysis of data.
Collaborator Contribution As part of the ongoing collaboration, we provide knowledge and expertise around ecotoxicology to each other.
Impact An NSF Eager Grant application in the US. Further publications on the way and more data generation and analysis.
Start Year 2018
 
Description Nimbios 
Organisation Oak Ridge National Laboratory
Country United States 
Sector Public 
PI Contribution Provide knowledge and techniques for molecular analyses of Daphnia magna. Train PostDoc and Collaborator in RNA extraction and subsequent analysis of data.
Collaborator Contribution As part of the ongoing collaboration, we provide knowledge and expertise around ecotoxicology to each other.
Impact An NSF Eager Grant application in the US. Further publications on the way and more data generation and analysis.
Start Year 2018
 
Description Nimbios 
Organisation US Army Research Lab
Department Engineer Research and Development Center
Country United States 
Sector Public 
PI Contribution Provide knowledge and techniques for molecular analyses of Daphnia magna. Train PostDoc and Collaborator in RNA extraction and subsequent analysis of data.
Collaborator Contribution As part of the ongoing collaboration, we provide knowledge and expertise around ecotoxicology to each other.
Impact An NSF Eager Grant application in the US. Further publications on the way and more data generation and analysis.
Start Year 2018
 
Description Nimbios 
Organisation University of California, Santa Barbara
Country United States 
Sector Academic/University 
PI Contribution Provide knowledge and techniques for molecular analyses of Daphnia magna. Train PostDoc and Collaborator in RNA extraction and subsequent analysis of data.
Collaborator Contribution As part of the ongoing collaboration, we provide knowledge and expertise around ecotoxicology to each other.
Impact An NSF Eager Grant application in the US. Further publications on the way and more data generation and analysis.
Start Year 2018
 
Title EPIC Web Interface 
Description The EPIC-db which is the database and the epic web front work closely together. They store all the information developed as part of this project and provide a web interface for interacting with the data. All graphs are build on the fly and provided in high quality svg graphics which allows them to be scaled to any size available. Further development is currently ongoing. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact It allows quick and easy entry of data and analysis. 
URL http://epic.liverpool.ac.uk
 
Description 13th SETAC Europe Special Science Symposium on the Extrapolation of Effects Across Biological Levels: Challenges to Implement Scientific Approaches in Regulation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact A special science symposium to which I was invited to present results regarding the linkage between molecular responses and dynamic energy budget modelling. The group was very diverse including regulatory representatives (ECHA, PHE, EA, EPA), Industry, and researchers were present.
Year(s) Of Engagement Activity 2018
 
Description NIMBioS sponsored working group "Modeling Molecules-to-Organisms" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A 2 year work group sponsored by NIMBIOS to further develop the application of Dynamic Energy Budget models, a type of models used to link effect on feeding and reproduction to population outcomes, to the Adverse Outcome Pathway (AOP) concept. This work group is currently underway and aims to develop book chapters and papers throughout the 2 year running period to provide guidance documents to enable the use of modelling for AOP development.
Year(s) Of Engagement Activity 2015,2016
URL http://www.nimbios.org/workinggroups/WG_m2o
 
Description OECD Working Party on Chemicals, Pesticides and Biotechnology 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact I was the OECD representative for the UK for the Working Party on Chemicals, Pesticides and Biotechnology. A large number of countries were represented and talked about the use of AOPs and regulatory components on an international scale.
Year(s) Of Engagement Activity 2018
 
Description Stoichiometric Ecotoxicology (NIMBIOS) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Accurately assessing the risks of contaminants requires more than an understanding of the effects of contaminants on individual organisms, but requires further understanding of complex ecological interactions, elemental cycling, and interactive effects of natural and contaminant stressors. There is increasing evidence that organisms experience interactive effects of contaminant stressors and food conditions, such as resource stoichiometry and nutrient availability. The development of ecotoxicological models over the last few decades have significantly contributed to interpreting how contaminants impact organisms and cycle through food webs. Existing modeling efforts take a variety of approaches to predict the effects of diverse chemical contaminants on organismal growth and survival; however, current models do not consider dynamical interactive effects of contaminant stressors and stoichiometric constraints, such as nutrient/light availability and food quality. This investigative workshop provided a forum for discussions of incorporating multiple essential elements and contaminants in ecotoxicological models. Discussions and breakout sessions throughout the workshop shed light on nutrient and chemical contaminant cycling with the aim of helping to improve toxicological risk assessment protocols. The objectives for the workshop included:

Discussing the importance of linking Ecological Stoichiometry with Ecotoxicology and summarizing the current state of the synthesis of these two theories
Formulating a series of empirically testable and robust models of individual and population dynamics subject to stoichiometric constraints and contaminant stressors
Identifying future directions for models to be used in practice for ecological risk assessments and determining areas where empirical data are lacking in order to parameterize, test, and improve the models
Year(s) Of Engagement Activity 2018
URL http://www.nimbios.org/workshops/WS_ecotox
 
Description Workshop on Developing Integrated Multi-level models of the Environment 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A 1.5 day workshop organised by myself and a colleague to address the issue of integration, interrogation and interpretation of multi-level datasets currently created by large consortia meetings. The workshop is sponsored by an STFC/NERC grant and brings together experts across the world to create a guidance document on the use of computational approaches in large consortia grants, how to maximize integration and hence maximize interpretation of the underlying biology.
Year(s) Of Engagement Activity 2016
 
Description Workshop on Epigenetics in Environmental Science - from mechanisms to regulation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact A workshop was held on the Epigenetics in Environmental science. The output will be a paper that is due to come out in the near future. Governmental representatives (Public Health England, Environmental Protection Agency USA, and Swedish Environmental Agency) were present.
Year(s) Of Engagement Activity 2019