Mutagenesis Advance Access originally published online on October 18, 2007
Mutagenesis 2007 22(6):425-427; doi:10.1093/mutage/gem037
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Epigenomics and disease, 10th anniversary winter meeting of the UK Molecular Epidemiology Group (MEG), The Royal Statistical Society, London, UK, 8th December 2006
Biomedical Sciences Unit, Department of Biological Sciences, Lancaster University, Lancaster LA1 4YQ, UK
Meeting participants: Manel Esteller (Spanish National Cancer Research Centre, Spain), Zdenko Herceg (International Agency for Research on Cancer, France), John C. Mathers (University of Newcastle, UK), Saverio Minucci (European Institute of Oncology, Italy), Fei Ling Lim (Syngenta Central Toxicology Laboratory, UK) and James E. Trosko (Michigan State University, USA).
Organizing UK MEG committee: John E. Hesketh (University of Newcastle, UK), F.L.M. (Lancaster University, UK), David H. Phillips (Institute of Cancer Research, UK), Michael N. Routledge (University of Leeds, UK), Lesley Rushton (Imperial College, UK) and Paolo Vineis (Imperial College, UK).
An organism has a unique genome but may have different tissue-specific epigenomes. Distinct from the genotype, epigenomics encompasses the modulation of gene activity through particular global chromatin methylation patterns or histone modifications; these may be known as epigenetic marks. The chromatin pattern of epigenetic marks is modifiable over a lifespan and may influence disease progression at a particular site. The meeting aim was to discuss the role of epigenomics in the aetiology of disease, particularly cancer. Epigenetic marks might be modifiable through dietary intake of methyl donors and aberrant patterns may underlie phenotypical changes resulting in chronic diseases such as cancer. DNA methylation patterns or histone modifications are potentially reversible, but, in certain circumstances, such marks become imprinted and give rise to trans-generational effects. Other reversible effects influencing disease occurrence might be inhibition of gap junction intracellular communication. Environmental and/or dietary factors play a pivotal role in the aetiology of cancer. Most cancers require a mutagenic initiation step. However, it is now recognized that an aberrant pattern of epigenetic marks may link the initiating mutation to the gene expression profile of a disease phenotype. This workshop stressed the need for a human epigenomic project out of which specific aberrant patterns of epigenetic marks might be developed as novel predictors to facilitate the implementation of future disease prevention strategies, to lend new insights into aetiology of disease, to allow more exact diagnosis and to develop better-targeted therapeutic regimens.
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Introduction |
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 Top Introduction Towards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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Epigenomics encompasses the modulation of gene activity through global genomic methylation patterns or histone modifications that may be known as epigenetic marks. Alterations in epigenetic marking influence the phenotypical expression of a genotype and such chromatin modifications probably play a central role in chronic diseases such as cancer. They may also give rise to heritable changes in gene function in the absence of a change in base sequence.
Epigenetic information (or marking) is principally stored and propagated via methylation of DNA at cytosine residues; this gives rise to 5-methylcytosine (5-MC). Cytosine methylation mostly occurs at genomic sites known as CpG islands and is generally associated with gene silencing, for instance, of tumour suppressor genes (1
). Perturbation of DNA methylation status alters the cellular gene expression profile, which in turn leads to alterations in phenotype. Reversal of methylation at hypermethylated sites may restore expression of silenced genes. An altered pattern of epigenetic markings may also give rise to trans-generational effects that are modifiable through dietary or chemical intervention (2). To date, DNA methylation has been the most intensively studied epigenetic mark.
Epigenetic marking of the genome also includes post-translational modification of the octet of histones (i.e. the nucleosome) around which the DNA is wrapped in the nucleus. Histone tails may be methylated (leading to gene silencing) or acetylated (leading to gene activation). These modifications influence chromatin structure and regulate gene expression. Unlike genotype, the pattern of epigenetic marks may vary over time in an inter- and intra-cellular fashion within an organism.
There are some 35 000 genes in the human genome but only a subset, modifiable by environmental factors that can alter the pattern of epigenetic marks, is expressed in each cell. For instance, infant monozygotic (MZ) twins have similar patterns of epigenetic marks across different tissue types whereas middle-aged twins exhibit remarkable differences (3). Also, such differences in chromatin patterns are more profound in older MZ twins who led different lifestyles in different environments, e.g. rural versus urban. This strongly suggests that environmental factors play a significant role in epigenetic drift. Human tumours exhibit profound, but specific, alterations in the pattern of epigenetic marks. Characterizing such aberrant patterns in epigenetic marks in different tumours can identify those alterations associated with a particular prognostic outcome or therapeutic strategy.
This workshop set out to discuss the new insights into mechanisms of cancer causation that are being identified through the field of epigenomics. One of the major current questions is how alterations in epigenetic marks drive disease progression and whether the identification of specific aberrant patterns might be used as predictors of risk in disease prevention strategies. It also set out to stress the fact that in disease causation and progression, altered epigenetic patterns are an important component that also includes more traditionally investigated mechanisms such as initiating mutagenesis. These different areas need to be studied in combination, not isolation, in order to properly understand disease.
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Towards a human cancer epigenome |
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TopIntroductionTowards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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The first session, chaired by Paolo Vineis (Imperial College), started with the keynote lecture entitled ‘Towards a human cancer epigenome’ delivered by Manel Esteller (Spanish National Cancer Research Centre). In human cancer, aberrant patterns in epigenetic marks occur in genes in all cellular pathways including DNA repair (e.g. MGMT, BRCA1), cell cycle (e.g. p16INK4a, p14ARF), apoptosis (e.g. DAPK, TMS1), hormone receptors (e.g. ER, PR), cell adherence (e.g. CDH1, TIMP3), detoxification (e.g. GSTP1) and many more (e.g. APC, LKB1); it is now possible to establish a comprehensive database of these specific alterations (4
). An epigenetic alteration can give rise to a disease-predisposing mutator pathway. For instance, methylation-mediated silencing of MGMT leads to G 
A transition mutations (e.g. seen in lung cancer) (5). However, knowing this information opens up a novel therapeutic strategy as tumours exhibiting MGMT silencing (e.g. gliomas) are more susceptible to alkylating agents (6).
Hypermethylation can be observed in hereditary tumours, where it may account for the ‘second hit’ of the tumour suppressor gene. Genomic screenings for hypermethylated genes are identifying new candidate tumour suppressor genes. In a particular tumour, 5-MC DNA content and the number of hypermethylated CpG islands is not random; environmental factors and genetic predisposition are involved (3). The human genome project of the late 1990s may be the prelude to the advent of the epigenomics era. There is now a need for a human epigenome project and a starting point for such a project is an examination of the epigenome of simple organisms (e.g. human papilloma virus, hepatitis B virus and Epstein-Barr virus) (7).
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A genetic versus epigenetic mechanism of cancer |
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TopIntroductionTowards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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James Trosko (Michigan State University) then put forward the concept ‘"Chemical carcinogens as mutagens" and "molecular epidemiology of cancer" are bankrupt paradigms: stem cells, altered cell–cell communication and epigenetic mechanisms as ignored concepts’. Rather than genotoxic and/or mutagenic events, more important mechanisms in disease progression might be disruption of cellular homeostasis that might modulate adult stem cell pools, e.g. through inhibition of gap junction intercellular communication. Non-genotoxic, but possible promoting, agents that might modulate patterns of epigenetic marks (e.g. 12-O-tetradecanoylphorbol-13-acetate, phenobarbital and polybrominated biphenyls) characteristically generate reversible non-mutagenic toxicity if over a long exposure time they reach a threshold concentration (8
,9). The need to focus more on factors modifying whole systems rather than examining lesions at the molecular level was stressed because one can never eliminate the initiation phase of carcinogenesis (8).
Zdenko Herceg (International Agency for Research on Cancer) continued and discussed ‘Studies on epigenetics and lung cancer’. Carcinogenesis is a complex multistage process mostly associated with environment and/or diet, and a genetic component (e.g. a mutation) is always present (10). As cancer is most often a consequence of environment, it is therefore preventable and there is thus a need to understand mechanisms (10). Currently, in the absence of statistically robust studies, little is known regarding the contribution of aberrant patterns in epigenetic marks, the role of ‘epimutagens’ in the environment, or the contribution of different dietary components in disease causation.
However, there is compelling evidence that gene-specific patterns in DNA methylation may now be applied to epidemiological studies. For instance, the P16 promoter region is specifically heavily methylated in lung cancer tissue compared to normal (11). Elevations in methylation level at this site are reversible. Thus, they may be exploitable as a predictor of risk to this disease long before its onset. Knowing the methylation level at specific ‘sites of risk’ may allow specific quantitative assessments of particular patterns in epigenetic marks and suggest where reductions in chemical carcinogen exposure is a possible intervention strategy.
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Epigenetic alterations, biomarkers and disease |
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TopIntroductionTowards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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The afternoon session was chaired by John Hesketh (University of Newcastle) and started with a talk entitled ‘Epigenetics in the study of chronic diseases’ delivered by Fei Ling Lim (Syngenta Central Toxicology Laboratory). A model to study the effect of differences in epigenetic marks is the viable yellow agouti (Avy) mouse; these mice are genetically identical (isogenic) but because of differences in methylation patterns, they may exhibit different coat colour, adiposity, glucose tolerance and tumour susceptibility (12
). The Avy mouse harbours a retrotransposon (a cryptic promoter) in the agouti gene. CpG methylation in this region varies, is inversely correlated with ectopic agouti expression and causes a wide variability in individual coat colour among littermates. Placing mother Avy mice on a diet supplemented with folic acid, vitamin B12, choline or betaine alters the coat colour of offspring (13,14). Such diet-derived methyl donors are necessary for the synthesis of S-adenosylmethionine required for CpG methylation. These model studies have laid the basis for understanding the role that specific patterns of epigenetic marks play in development and susceptibility to disease.
Saverio Minucci (European Institute of Oncology) discussed ‘Chromatin alterations in tumorigenesis’ in a murine model system of acute myeloid leukaemia. Unlike solid tumours, an initial characteristic of leukaemia is the presence of chromosomal translocations that give rise to fusion proteins (15–17). Altering gene expression in this model results in promyelocytic leukaemia cells arrested at a specific stage of myeloid differentiation within the stem cell compartment (15). The fusion protein is PML–RAR; this acts as a transcription factor and is able to bind response elements but recruits chromatin-modifying enzymes differently to normal.
Binding of PML–RAR alters the epigenetic profile and gives rise to a heterochromatin-like state refractory to differentiating stimuli (16). For solid tumours, chromatin changes might also be a driver in disease progression. Novel technologies now allow the systematic analysis of genome-wide alterations in factors that influence the pattern of epigenetic marks and may play a role in the design of optimized anti-cancer treatments, e.g. histone deacetylase inhibitors (17).
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The nutritional environment and epigenetic marking |
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TopIntroductionTowards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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In the final presentation, John Mathers (University of Newcastle) considered ‘Nutrition and epigenetics—how the genome learns from experience’. Environment matters in terms of phenotype; this is seen in the requirement of vernalization to down-regulate expression of genes required for flower development (18
).
Mathers suggested that there are four Rs that govern how epigenetic marks occur and are expressed. These comprise how the genome Receives environmental stimuli, Records and Remembers that information through successive cell generations and Reveals effects of those stimuli through changes in gene expression (19). For instance, mutations in tumour suppressor genes in bowel cancer may be causative but so may silencing of such genes by methylation. Specific patterns in epigenetic marks may give rise to markers in colonocytes long before onset of symptomatic disease. It is possible to quantify elevated gene methylation at specific CpGs (e.g. HPP1) in individuals in the absence of apparent colonic cancer (20) or in the ‘normal’ mucosa of ulcerative colitis patients (21). Dietary intake of tea polyphenols [e.g. (–)-epigallocatechin-3-gallate], folate or diallyl disulphide may be plausible intervention strategies (21–23). Evidence supporting this notion was the observation that higher intakes of dietary fibre, leading to greater production of butyrate (a C-4 fatty acid and potent inhibitor of histone deacetylase), may protect against bowel cancer (24).
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Conclusions |
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TopIntroductionTowards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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Specific aberrant patterns of epigenetic marks contribute to predisposition to and development of disease. This specificity raises the possibility that they may function as predictors of risk before the onset of disease, as prognostic indicators or may facilitate the determination of therapeutic strategies. Epigenetic markers (e.g. lung cancer) may be detectable years before the clinical manifestation of disease (11
). However, genetic alterations such as mutations are also pivotal events in cancer; it is important to study the role of genetic alterations and patterns of epigenetic marks in combination. The precise contribution of altered patterns in epigenetic marks to the development of human cancers remains largely unknown. Epidemiological studies that have the power to identify these aberrant but specific patterns remain to be conducted; this could give rise to ‘epigenomic polymorphisms’ associated with risk stratification dependent on degree of methylation or other chromatin-modifying marks. Thus, it will be important to understand the role of epigenetic mechanisms in normal cellular processes and abnormal events that lead to oncogenic transformation and tumour development. A human epigenome project would have profound consequences for identifying populations at risk, lend new insights into the mechanistic basis of disease causation, allow for more precise diagnosis and facilitate the implementation of targeted treatment regimens. |
Funding |
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TopIntroductionTowards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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United Kingdom Environmental Mutagen Society; ECNIS.
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Acknowledgments |
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We are most grateful to Jenny Duckmanton for administrative organization and Michael J. Walsh for assistance. Also acknowledged is the contribution made by participants to the preparation of this article through the prior provision of abstracts.
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Notes |
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To whom correspondence should be addressed. Tel: +44 1524 594505; Fax: +44 1524 593192; Email: f.martin{at}lancaster.ac.uk
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References |
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TopIntroductionTowards a human cancer...A genetic versus epigenetic...Epigenetic alterations,...The nutritional environment and...ConclusionsFundingReferences |
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Received on August 19, 2007; revised on August 22, 2007; accepted on August 23, 2007.
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