Workshop Report 30

Session 2: Generating a Prioritised Research Agenda

Session 2 (afternoon) consisted of one action: “Generate a prioritised research agenda”. Each brainstorm group discussed this topic and were tasked with preparing an outline request for proposals on the priority topic/theme that resulted from their discussion. At plenary, participants again regrouped and the moderators summarised the outcomes of the discussion.
Professor Gant gave the following guidance, summarised from Day 1 discussions, to provide context for the brainstorm:
Mechanistic understanding – what do we need to know that will assist regulatory activity and product development?
Do we need to further repeat and verify former research findings, e.g. vinclozolin?
How do we get to dose-response relationships and causation?
Are there likely to be thresholds? Or are responses likely to be non-threshold vs. genotoxins?
Epidemiology: is it necessary and if so, what are we looking for?
What more do we need to know that will be of practical application?
The following research proposals were developed by the breakout groups:
Breakout Group 1
Objective:
Identify sensitive and predictive markers for latent adverse outcomes following early life exposure. Evaluate feasibility of these epigenetic markers for relevance of human health risk assessment.
Scope:
After sufficient literature review, the researchers will submit a proposal focused on identifying sensitive, reliable, and predictive markers for latent adverse reproductive outcomes following early-life chemical exposure. Protocols for analysis and dose-level selection will need to be scientifically justified. Dose levels will need to incorporate a high-dose group which is known to elicit a specific adverse outcome, as well as a dose level that is expected to determine a phenotypic NOAEL. The researchers will identify dose-response curves and temporal relationships for epigenetic, transcriptomic, and apical outcomes. Temporal relationships will be used to assess persistence of the epigenomic effect and memory and relation to the adverse outcome. The researchers will need to compare the biomarkers for specific adverse outcomes across molecules that are known to be true positives and negatives for the phenotypic outcome. It is recommended that the highest level and most cost effective methods currently available are used and scientifically justified bioinformatics approaches. It is recommended to use 5+ animals per dose group.
Chemical Examples:
Dexamethasone and fertility (male and female germline).
Phthalates and male reproductive effects.
Dioxin and fertility.
Oestrogen and female puberty.
Deliverables:
Cost and Timing/Duration of Project: USD 500,000. 3 years.
Partnering/Co-funding: It is recommended to have a consortium application with several different scientists with relevant multidisciplinary expertise.
Breakout Group 2
Title: Epigenetic Normality across different laboratories and across different species.
Background:
There are reports of in utero exposure causing effects in the adult suggesting a role for an epigenetic-mediated toxicity. Up to now we do not know the normal epigenetic landscape and how this epigenetic landscape can be influenced by chemical exposure. Companies would be willing to provide samples according to GLP standards to facilitate this work.
Objectives:
What is the normal epigenetic landscape in different species and in different laboratories?
Does in utero exposure result in persistent changes in the adult?
Scope:
Examine epigenomic changes (methylation and miRNA patterns), transcriptome (RNAseq), and histology in the target tissue at different stages in life (in utero, postnatal, prior to the adverse effect being observed, at time the adverse effect is observed).
Priority target organs are chemical dependent but should focus on sex organs for reproductive biology.
Reproducibility across different labs: Are there different epigenomic patterns among labs in the target tissue from control organisms?
Breakout Group 3
RfP 1:
Title: Enabling Resources in a Data Analysis and Coordination Centre.
Background:
In order to be able to perform toxicological studies in model organisms relevant to human health there is a need to have enabling resources that involve data management and analysis standardisation.
Scope:
This Data and Analysis Coordination Centre should have the potential to generate new genomic data that could facilitate consortium investigator directed required data sets to include (but not restricted to) the development of model system genomic sources (e.g. rat) and single cell genomics and transcriptomics to enable understanding of cell and sub-cell composition issues in the cell type in the organism of interest: i.e. we expect integrated analysis in order to interpret interactions between genome, transcriptome and epigenome and how they reflect cellular sub-type proportional and physiological events.
Deliverables:
The data and Analysis Coordination Centre should develop protocols (standard operating procedures and data interpretation principals) to help others develop reproducible studies. This activity should be accompanied with a dissemination plan to share such protocols. Manage data to publicly recognised resources where they will continue to be available and updated.
RfP 2:
Title: An in vivo exposure model that will give reproducible apical endpoints that can be used for correlative studies involving molecular and cellular assays.
Objective:
The study should be of high confidence, reproducible and highly interpretable in terms of underlying high-confidence epigenetic events; therefore information should be gathered on the potential genomic, cellular and transcriptomic influences upon the epigenome that will allow the high-confidence identification of cell-innate epigenetic changes associated with the phenotype.
Scope:
Focus on early life exposure resulting in later onset of adverse endpoints with emphasis on reproductive toxicity but not restricted to fertility. Identify and justify the choice model compounds and the preferred model system. The use of validation using in vitro systems is encouraged to complement the in vivo systems. Longitudinal studies that enable the identification of permanent epigenetic changes (and therefore higher certainty of being associated with phenotype) are also encouraged. These studies should build towards future follow-up studies including the detailed description of the test system so that it can be reproduced in other laboratories and geographies.

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