Gene expressions

1. Gene-environment interaction:
the role of epigenetics
Marc Gunter, PhD
Reader in Cancer Epidemiology
School of Public Health
Imperial College London

2. Outline
•Defintion of Epigenetics
•Types of Epigenetic Modulation
•Epigenetic Phenomena
•Epigenetics and Cancer
•Impact of the Environment on Epigenetics
•Future Directions of Epigenetics

3. What is Epigenetics?
• Epigenetics is the study of inherited changes in
phenotype (appearance) or gene expression caused by
mechanisms other than changes in the underlying DNA
sequence.
• These changes may remain through cell divisions for
the remainder of the cell's life and may also last for multiple
generations.
• Changes in gene expression that do not involve
alterations in DNA base sequence

5. Epigenetic Modifications
•DNA Methylation
•Histone Modification (e.g. Acetylation, methylation)
•Non-coding RNAs (e.g. microRNA)
•All Regulate Gene Expression

6. Epigenetic Modifications
•DNA Methylation
• C-5 position of cytosine in CpG dinucleotides (Islands)

7. •~4% of cytosines are methylated
•70% - 80% of CpG cytosines are methylated
•Expected Frequency of CG = 4.4%
•Actual Frequency of CG = 1%
•~60% of genes have CpG island promoters, typically unmethylated
•DNA methylation represses transcription directly (inhibits TF binding)
•DNA methylation represses transcription indirectly by recruiting Me-CpG-binding proteins
Epigenetic Modification: DNA Methylation

8. - When histones are tagged, or acetylated, chromatin is open
and genes are potentially active;
- When histones are not chemically tagged, deacetylated, the
chromatin condenses and genes silenced.
Epigenetic Modification: Histone Modifications

9. Epigenetic Modification: Non-coding RNAs
A new mechanism for gene
regulation
• RNA which is not used for
making proteins (non-coding
RNA) can be cleaved and
used to inhibit protein-coding
RNAs
•siRNAs, microRNAs (~22
Nucleotides; fine tune gene
Expression)

10. Epigenetic-Regulated Phenomena
•Cellular Differentiation
• Totipotent cells become pluripotent cells of the embyro which
differentiate into specific lineages
•X-chromosome Inactivation
• Gene expression on one of the female X-chromosomes is
downregulated
• DNA methylation and histone modifications
•Imprinting
• Epigenetic marking of a locus on the basis of parental origin
• Results in monoallelic gene expression

11. H19
IGF2*
H19*
IGF2
Paternal
Imprinting
Maternal
Imprinting
Parental Imprinting

13. Epigenetics and Cancer
1. DNA methylation
•Gene specific hypermethylation (eg RASSF1, MLH1)
•Genome-wide hypomethylation (4% down to 2-3% of all
cytosines)
2.Histone Modifications
•Active vs Inactive histone marks
•Polycomb group gene silencing (H3-K27-me3)
•Growing data on the importance of epigenetics in the
aetiology and pathogenesis of cancer
Cancer Epigenetics Paradox: Global Loss of DNA methylation in addition to
locus-specific gain in methylation are causally linked to human cancer
Many cancer risk factors cause epigenetic modifications

14. DNA Methylation Influences Cancer
Processes
DNA
Repair
Hormonal
Regulation
Carcinogen
Metabolism
Apoptosis
Differentiation
Cell Cycle
DNA
Methylation

15. Epigenetics and The Environment
•Epigenetic changes can be inherited mitotically in
somatic cells
•Pre-natal and early post-natal exposures can result in
changes in risk of developing disease
• Nutrition
• Xenobiotic chemicals
• Behavioural Factors
• Reproductive Factors, Hormonal Exposures
•Epigenetic alterations may also be inherited
transgenerationally (developmental origins of adult-
onset disease)

16. Epigenetics and The Environment
–Prenatal environment
•Famine exposure, Folic acid use (Tobi et al HMG 2009,Steegers-Theunissen et al
Plos One 2009)
–Adult methylome
• Smoking, Diet (Breitling AMHG 2011, Zhang Journal of Nutrition 2010)
–Cancer methylome
• Alcohol and folate (Christensen et al Plos genetics 2010)
–Methylation variability between monozygotic twins increases
with age (Fraga et al PNAS 2005)

17. Mapping sequences with differential DNA methylation
between MZ twins.
Fraga M F et al. PNAS 2005;102:10604-10609

18. Smoking and DNA Methylation (In Vitro)
PlosOne 2010

19. Smoking and DNA methylation (In Vivo)
Vaissiere et al. Cancer Res 2009

20. Diet and gene promoter methylation in smokers

21. One-carbon metabolism and dietary methyl donors
DNA
methylation
SAM S-adenosylmethionine
Various dietary micronutrients can impact DNA methylation (e.g.
Folate, choline, Vitamin B)

22. 1-
3
H-Methyl
Acceptance
(%)
100
50
0
Day of Depletion
6 69
Jacob et al J. Nutr. 128:1204, 1998
Dietary Folate Deficiency Causes Hypomethylation in Human
Lymphocytes

23. In Utero Nutritional Exposure and Changes in Offspring
Phenotype

25. Dutch Hunger Winter 1944-1945
•Famine in The Netherlands towards the end of WWII-caused by Nazi
occupation (blockade) and severe winter; led to severe malnutrition in
Dutch population
•Dutch Famine Birth Cohort Study-prospectively studies offspring of
mothers who were exposed to the famine
•Offspring shown to be increased risk of diabetes, obesity, CVD
•Offspring were smaller than those born to non-exposed mothers and then
the children of these offspring were also, on average, smaller
• Suggestive of transgenerational inheritance-epigenetics

26. Difference in DNA methylation of CpG dinucleotides in siblings discordant for
periconceptional exposure to famine.
Tobi E W et al. Hum. Mol. Genet. 2009;18:4046-4053
•60 individuals pre-natally
exposed to famine
compared with matched,
unexposed siblings
•Investigated several
genes involved in
metabolism
•Positive difference
indicates higher
methylation level among
exposed individuals

27. Future Directions
•Characterization of the ‘epigenome’
• Relationship with environmental factors (signatures?)
• Do epigenetic marks mediate the association of environmental factors and
disease risk?
•Epigenome-wide association study for diseases such as cancer,
diabetes?
•Epigenetic marks as biomarkers of disease risk?
•Personalised medicine based on epigenetics?
•Will epigenetics be more relevant to human medicine/disease than
genetics?

28. Role for epigenetic mechanisms in the
pathogenesis of Type 2 diabetes.