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EMSG49: Investigation of normal variability and chemically induced epigenetic modifications – Deadline: February 29, 2008

Background

The emerging field of epigenetics can be defined as heritable changes in gene expression that occur without an alteration in DNA nucleotide sequence. Such changes may be mediated by direct DNA methylation and/or histone modification resulting in altered chromatin conformation and subsequent up- or down-regulation of gene expression. Since global alterations in DNA methylation patterns can potentially lead to changes in gene expression, epigenetic effects are physiologically relevant and highlight one mechanism in which an organism is able to adapt to environmental change. Furthermore, different epigenetic states between individuals can lead to altered susceptibility in the absence of DNA sequence alteration. There is little understanding of the normal state of the epigenome or what epigenetic changes of physiological relevance might occur as a result of exposure to environmental stressors such as industrial chemicals. It is even less clear if such changes can be used to identify potential health hazards posed by industrial chemicals.

In recent years there has been growing concern that epigenetic events may play a role in chemically and/or nutritionally driven adverse health effects; with particular focus towards reproductive toxicity and non-genotoxic carcinogenesis. The evidence that epigenetic changes influence environmentally induced disease has been concomitant with recent improvements in sensitivity and throughput for analyzing DNA methylation.
Within this framework, research proposals are requested to address the following areas:

  1. Gaining a better understanding of what constitutes the ”normal” landscape of epigenetic modification for example between species and strains; and
  2. How should the understanding of epigenetic modifications be factored into toxicological endpoint considerations and extrapolated to assess potential human health risks.

Although epigenetic changes include non-DNA methylation mechanisms, such as covalent histone modifications, microRNA interactions, and chromatin remodelling complexes, the current molecular techniques and high-throughput methodologies are most mature for DNA methylation analysis. Accordingly, the scope of investigation should be restricted to DNA methylation in the in vivo rodent animal model system.

Objectives

Until a solid framework for understanding the biology and variation in epigenetic status is established, it will not be possible to contextualize concerns about the relationship between adverse health effects and epigenetics. Specific concerns relate to the apparent "noise" (i.e., technical, biological, experimental, and spatial or temporal variability) of the experimental system, which sometimes can mask the induced "signal". Therefore, a research program addressing these areas will allow a better understanding of the contribution of epigenetic alterations to adverse toxicological events.

Phase 1: Study of Methylation and Demethylation Sites on DNA

Refine the landscape of "normal" DNA methylation variability with respect to many individual genes, as opposed to global methylation. Specific research areas of interest could include, but are not limited to, the following themes:

  • What is the inter- and intra-species variation of DNA methylation for key regulatory genes (e.g., tumor suppressors and oncogenes)?
  • What is the variability in DNA methylation patterns among different tissue types within a single animal? What is the variability within a single organ/tissue/cell in a single animal? How does the DNA methylation status change during the life span of the animal?
  • What is the range of DNA methylation patterns among different inbred animal strains? Is there an appreciable increase in variability among outbred strains?
  • Are DNA methylation changes part of normal homeostatic responses to environmental change or chemical challenge, and what is the dynamic range of such responses?

Phase 2: Epigenetic Stability & Pathological Change

Apply data generated in Phase 1 to provide a framework for chemically-induced DNA methylation alterations. Phenotypically anchor observed changes in DNA methylation with classical toxicity endpoints such as histopathology. Special attention should be paid to low dose effects. Specific research areas of interest could include, but are not limited to, the following themes:

  • What is the relationship between epigenetic changes and DNA mutation? When characterizing a phenotypic change, how does one verify the cause as epigenetic and not mutagenic?
  • Are there dose and time response relationships in epigenetic change in response to chemicals? How does one determine if a documented epigenetic change is the cause of, or result of, the identified phenotypic alteration?
  • Is there recovery/reversion of an induced epigenetic change?
  • Transgenerational effects
    • Are DNA methylation patterns heritable through the germ line?
    • Do DNA methylation patterns altered by parental toxicant exposure persist in unexposed F1 or F2 generation offspring?
    • Does toxicant exposure alter developmental imprinting? If so, how?
  • Carcinogenesis
    • Do alterations in global promoter methylation patterns, as a result of toxicant exposure, accelerate carcinogenesis through bypassing the traditional multi-step hypothesis of cancer progression with a single event affecting multiple loci and loss of heterozygosity?

 

Scope

It is recognized that it will not be possible, within the context of the current RfP, to address all of the themes identified in Phases 1 and 2. The applicants are encouraged to incorporate selected themes from both Phase 1 and Phase 2 to develop an integrated research programme.

  • Generate data to better understand normal epigenetic variability of DNA methylation in tissues, individuals, strains, and species. Make publicly available as a resource to help increase scientific understanding field.
  • Characterize epigenetic modifications (specifically DNA methylation) from relevant-dose chemical treatment.
  • Short interim reports on progress at 3 to 6-monthly intervals
  • Peer-reviewed publications and publicly accessible data
  • Oral or poster presentation(s) at international scientific meetings

 

 

 

Timing: Start Q2/2008, duration up to 36 months

LRI funding: Budget in the order of 750,000 Euro

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