Epigenetics and Environment

Environmental and Dietary Impacts on Epigenetics

Epigenetic Drift

• Epigenetic drift is an important concept (INS).

Lecture Plan

• Sources of epigenetic modifiers.
• Evidence that they modify the epigenome.
• Modifiers as preventative methods.

Sources of Epigenetic Modifiers

• Diet:
  • High-fat diet
  • Alcohol
  • Folate
  • Vitamins
  • Epigallocatechin-3-gallate (EGCG) (green tea)
  • Genistein (soybean)
  • Resveratrol

Sources of Epigenetic Modifiers - Carcinogens & Toxic Compounds

• Reference: Mathers et al., Adv Genet. 2010

Sources of Epigenetic Modifiers - Endocrine Disruptors, Infectious Agents & Behaviour

• Reference: Mathers et al., Adv Genet. 2010

DNA Methylation and Diet: Folate/Vitamins

• The folate cycle and its impact on DNA methylation.
• The diagram illustrates how folate, dietary protein, and vitamins contribute to the production of SAM (S-Adenosyl Methionine), a methyl donor crucial for DNA methylation.
• Key components and processes:
  • Folate Cycle: Involves the conversion of DHF (Dihydrofolate) to THF (Tetrahydrofolate).
  • Remethylation Cycle: Methionine is regenerated from Homocysteine using MS (Methionine Synthase) and B12.
  • Transulphuration Pathway: Homocysteine can also be converted to Cystathionine via CBS (Cystathionine-β-Synthase) and B6.
  • SAM: S-Adenosyl Methionine is formed which donates a methyl group to DNA, resulting in SAH (S-Adenosyl Homocysteine).
• Key enzymes:
  • Thymidylate Synthase
  • MTHFR (Methylene Tetrahydrofolate Reductase)

DNA Methylation

• DNA methylation is the only commonly occurring covalent modification of DNA.
• Enzymes involved: DNMT1, 3a, 3b.
• Conversion of Cytosine to 5-methylcytosine using SAM as a methyl donor, which then becomes SAH.
• $NH<em>2 O$ $4 \atop H$ $5 \atop 6$ \downarrow \atop 1 \atop 2 \atop 3 $NH</em>2 O$ $4 \atop {CH_3}$ $5 \atop 6$ \ Cytosine to 5-methylcytosine
• SAM to SA.

Folate and Agouti Mice

• Demonstration of how dietary folate levels can affect the phenotype of genetically identical mice.

Folate and Agouti - Low Folate/B12 vs. High Folate/B12

• Comparison of mice with low folate/B12 levels versus those with high folate/B12 levels.

Folate and Agouti - IAP and Methyl Availability

• IAP (Intracisternal A Particle): An endogenous retroelement.
• High methyl availability leads to increased methylation of the IAP.
• The Agouti gene region includes coding and non-coding exons and is involved in paracrine signaling.
  *Reference: Morgan et al, Nat Genet. 1999

High Methylation = Happy Mouse

• High methylation is associated with a normal phenotype.

Folate and Agouti - Low Methyl Availability

• Low methyl availability results in decreased methylation of the IAP.
  *Reference: Morgan et al, Nat Genet. 1999

Low Methylation = Unhappy Mouse

• Low methylation is associated with:
  • Overweight
  • Diabetes
  • Cancer prone

Smoking and DNA Methylation

• Smoking leads to large-scale, reproducible changes in DNA methylation.
• These changes generally revert towards normal after smoking cessation.
• Meta-analysis identified 2623 CpG sites (out of 18,760 CpG sites analyzed).
  *Reference: Joehanes et al, Circ Cardiovasc Genet. 2016

Smoking Effects in Children

• Similar effects are observed in children exposed to smoking in utero, particularly affecting the AHRR (Aryl Hydrocarbon Receptor Repressor) gene.
• Meta-analysis identified 568 CpG sites (out of 6073 CpG sites analyzed).
  *Reference: Joubert et al, Am J Hum Genet. 2016

Smoking - Prediction of Lung Cancer Based on AHRR Methylation

• Prediction of lung cancer risk based on AHRR (cg05575921) methylation levels.
• Observed and predicted 6-year cumulative incidence of lung cancer based on quintiles of AHRR methylation.
• The association between AHRR methylation and lung cancer risk is significant, as indicated by the log-rank trend test ($p = 2 Imes 10^{-7}$).
  *Reference: Bojesen et al, Thorax. 2017

Developmental Origins of Health and Disease (DOHaD)

• Exposure to specific environments or diets early in life (or in utero) can increase susceptibility to chronic diseases later in life.

Dutch Hunger Winter

• 1944-45 famine exposure in utero led to higher rates of obesity, diabetes, and heart disease.
• Effects depend on the timing of exposure:
  • First trimester: Associated with obesity, diabetes, heart disease, schizophrenia.
  • Last trimester: Associated with smaller size but lower levels of obesity.

Dutch Hunger Winter - IGF2 Methylation

• Impact of famine exposure during early vs. late gestation on IGF2 methylation.
• Ration levels (kcal/day) are correlated with changes in methylation.
  *Reference: Heijmans et al. PNAS 2008

Dutch Hunger Winter - Genome-Wide Study

• Genome-wide study of methylation differences in siblings exposed vs. unexposed to famine.
• Assessment of 24 pairs.
• Identification of 181 differentially methylated regions (DMRs).
  *Reference: Tobi et al. Nat Comm 2014

Dutch Hunger Winter - DNA Methylation Differences

• Analysis of average within-pair DNA methylation differences and their correlation with daily government rations (kcal per day).
• Specific genes (CDH23, RFTN1, CPT1A, SMAD7, INSR, KLF13) show differential methylation patterns.
  *Reference: Tobi et al. Nat Comm 2014

Endocrine Disruptors

• Bisphenol A: Used in plastic manufacture.
• Vinclozolin: Fungicide.
• Diethylstilbestrol: Synthetic hormone.

Transgenerational Inheritance

• Concept of inheritance patterns beyond the directly exposed individuals.

Transgenerational Inheritance - Endocrine Disruptor Exposure

• Exposure of a gestating female (F0) to endocrine disruptors can affect the germline of F1 and subsequent generations (F2, F3).
• F3 is the first unexposed generation, representing a transgenerational effect.
  *Reference: Skinner 2016, Nat Rev Endocrin

Transgenerational Inheritance - Vinclozolin Exposure

• Exposure to Vinclozolin (F0) leads to:
  • F3: Alterations in sperm motility.
  • Associated alterations in DNA methylation.
  • Some loci can escape early developmental re-programming.
    *Reference: Skinner 2016, Nat Rev Endocrin

Behaviour and Epigenetics

Should You Lick Your Baby?

Lick Babies Happy? - Maternal Grooming in Rats

• Licking and grooming behavior is normal mothering behavior in rats.
• Variations exist in the extent of this behavior among rats.
• Licking and grooming behavior is associated with reduced stress in adulthood.
• This is associated with increased expression of GR (Glucocorticoid Receptor) in the hippocampus.
  *Reference: Weaver et al, Nature Neuroscience 2004

Stress Response - Corticosterone Levels

• Corticosterone levels (stress hormone) in rats with different licking and grooming (LG/ABN) behaviors.
• Impact of TSA (Trichostatin A, a histone deacetylase inhibitor) on stress response.

Methylation and Grooming - CpG Dinucleotides

• DNA methylation patterns in the hippocampus of rats with different licking and grooming behaviors.
• Analysis of CpG dinucleotides in the NGFI-A (EGR1) binding region.
  *Reference: Weaver et al, Nature Neuroscience 2004

Methylation and Grooming - C-methylation

• Comparison of C-methylation (%) in low-LG/ABN versus high-LG/ABN rats across different CpG dinucleotides.
  *Reference: Weaver et al, Nature Neuroscience 2004

Effect of Early Life Trauma - Humans

• Glucocorticoid receptor (GR) (NR3C1) methylation is associated with depression.
• Early life events (child abuse) increase the risk of disease in adults.
• Potential role for FKBP5 (polymorphism in GR site associated with increased risk).

FKBP5 Methylation

• DNA methylation patterns of FKBP5 in individuals with and without trauma.
• Impact of FKBP5 rs1360780 genotype on methylation levels.
• Similar effects observed in vitro with Dexamethasone.
  *Reference: Klengel et al 2013, Nat Neuroscience

FKBP5 Post Cancer Treatment

• Childhood cancer treatment is associated with increased chronic disease, including psychiatric illness.
• Potential link to early life trauma and treatment with dexamethasone.

FKBP5 Methylation After Cancer Treatment

• FKBP5 methylation levels in controls versus patients with solid tumors (Solid) and acute lymphoblastic leukemia (ALL).
  *Reference: Martha Lenaghan - 3rd year BMS

Epigenetic Modifiers and Preventative Medicine

DNA Methylation and Aging

• Comparison of DNA methylation patterns in "young" versus "old" DNA.
• Changes in CpG island methylation.

DNA Methylation and Aging

• DNA methylation predicts “biological” age, not chronological age.
• It predicts susceptibility to chronic disease and life expectancy.
• Possible intervention: Reverse methylation to extend lifespan?

Can Reversing Epigenetic Change Reverse Aging?

Can Reversing DNA Methylation Change Reverse Aging?

• The link between methylation and aging.

Methylation Changes in B Cells

• Methylation changes in B cells: Naive vs. Memory vs. Class-switched Memory B cells.
• B cells can live for many years and keep proliferating.
  *Reference: Oakes et al 2016

Methylation Changes in B Cells - Naive vs. CLL

• Changes in DNA methylation in B cells comparing Naive vs. CLL (Chronic Lymphocytic Leukemia) cells.
• Changes in DNA methylation in B cells comparing Naive vs. Memory cells.
• Specific genes (FOXD3, ID4, DAPK1, HOXA4) show differential methylation.
  *Reference: Oakes et al 2016

Methylation Changes in B Cells and Proliferation

• Alterations in DNA methylation can be related to proliferation.
• Not necessarily related to loss of function.
• Increased aging = increased proliferation.

HDAC - SIRT1

• HDAC = Histone deacetylase, NAD = Nicotinamide adenine dinucleotide, SIRT = Sirtuin

SIRT1 / sir2 – C. elegans and lifespan

• Effect of SIRT1/sir2 overexpression on lifespan in C. elegans.
  *Reference: Tissenbaum & Guarente, Nature 2001

SIRT1/sir2 - Drosophila and Survivorship

• Impact of SIRT1/sir2 on survivorship in Drosophila.
• Effects of Resveratrol (res) supplementation.
  *Reference: Wood et al, Nature 2004

SIRT1/sir2 - Drosophila and Survivorship - Caloric Restriction

• Impact of SIRT1/sir2 on survivorship in Drosophila under different caloric restriction conditions.
  *Reference: Wood et al, Nature 2004

Should I Starve Myself Healthy? - Caloric Restriction

• Potential benefits of caloric restriction for various conditions including:
  • Mood
  • Brain injury
  • Diabetes
  • Heart disease
  • Osteoporosis
  • Liver disease

Caloric Restriction and SIRT1's effect on survival

• The relationship between caloric restriction, SIRT1, and survival in mice.

Machado–Joseph Disease

• Also known as spinocerebellar ataxia type 3.
• Progressive cerebellar ataxia.
• Results in lack of muscle control and coordination of the upper and lower extremities.

Machado-Joseph Disease - Cerebellar SIRT1 mRNA Levels

• SIRT1 mRNA levels in the cerebellum of wild-type (WT) and transgenic MJD mice under ad libitum (AL) and caloric restriction (CR) conditions.
  *Reference: Cunha-Santos et al, 2016 Nat. Commun.

Machado–Joseph Disease and SIRT1

• SIRT1 levels are rescued by caloric restriction (CR).
• Significant improvement in symptoms with increased SIRT1 levels.
• Can be replicated by genetic overexpression of SIRT1.
• Resveratrol is in phase 2 clinical trial for Friedreich Ataxia.
  *Reference: Cunha-Santos et al, 2016 Nat. Commun.

Epigenetics Summary

• Key epigenetic modifications:
  • DNA methylation
  • Histone modification
• Epigenetic mechanisms are heritable but labile.
• They can be influenced by a wide variety of exposures including diet, toxins, and behavior.

Epigenetics Summary

• Epigenetic mechanisms can act as “sensors” that modulate the impact of diet/environment on chronic disease.
• Animal models demonstrate that genetic or pharmacological modulation of epigenetic mechanisms can alter susceptibility to age-related chronic disease.
• Question: Can modulating the human epigenome prevent or reduce chronic disease in humans?