Epigenetics and Environmental Factors

Environmental and Dietary Impacts on Epigenetics

Epigenetics Drift

T-VINS

Lecture Plan

• Sources of epigenetic modifiers

• Evidence that they modify epigenome

• Modifiers as preventative methods

Sources of Epigenetic Modifiers

• Diet:

  • High fat diet

  • Alcohol

  • Folate

  • Vitamins

  • Epigallocatechin-3-gallate (EGCG) (green tea)

  • Genistein (soy bean)

  • Resveratrol

Sources of Epigenetic Modifiers: Carcinogens and Toxic Compounds

Sources of Epigenetic Modifiers: Endocrine Disruptors, Infectious Agents, and Behaviour

DNA Methylation and Diet: Folate/Vitamins

Folate Cycle and DNA Methylation

This slide illustrates the folate cycle and its connection to DNA methylation. The cycle involves dietary folate being converted into various forms, including dihydrofolate (DHF) and tetrahydrofolate (THF). THF is essential for several metabolic processes, including the synthesis of thymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP), a step crucial for DNA synthesis.

• Key Components & Reactions: Dietary protein contributes to methionine, which is then converted to S-Adenosyl Methionine (SAM). $SAM$ is a methyl donor utilized by methyltransferases to methylate DNA (R to RCH3). This process creates S-Adenosyl Homocysteine (SAH).

• Enzymes: MTHFR (Methylene Tetrahydrofolate Reductase). CBS (Cystathionine-β-Synthase).

• DNA Methylation: The diagram shows the transfer of a methyl group (CH3) from SAM to DNA, a process catalyzed by methyltransferases. This is a critical epigenetic modification, influencing gene expression.

• Other pathways: Transulphuration pathway converts homocysteine to cysteine with the help of B6. Other connected cycles are protein synthesis, urea cycle.

DNA Methylation

• DNA methylation is the only commonly occurring covalent modification of DNA.

• Key enzymes involved are DNMT1, 3a, and 3b.

• The process involves the addition of a methyl group (CH3) to cytosine, converting it into 5-methylcytosine.

$NH2 O 4 H 5 6 1 2 3 NH2 O 4 CH3 5 6 1 2 3 Cytosine 5-methylcytosine SAM SAH$

Folate and Agouti Mice

• Two genetically identical mice are shown, highlighting the impact of folate on phenotype. These mice are the same age.

• Reference: Waterland and Jirtle, Mol Cell Biol. 2003

Folate and Agouti Mice - Diet and Phenotype

• Low Folate/B12: Mouse with a yellow coat color, indicating low methylation.

• High Folate/B12: Mouse with a brown coat color, indicating high methylation.

• These differences arise due to varying levels of methyl availability affecting the Agouti gene.

Agouti Gene and Methylation

• The Agouti gene contains an IAP (Intracisternal A Particle), which is an inverted repeat. It contains coding and non-coding exons.

• High Methyl Availability: Leads to increased methylation of the IAP.

• Reference: Morgan et al, Nat Genet. 1999

High Methylation Effects

• High methylation leads to a "happy mouse".

Agouti Gene and Methylation - Low Methyl Availability

• Low Methyl Availability: Results in decreased methylation of the IAP.

• Reference: Morgan et al, Nat Genet. 1999

Low Methylation Effects

• Low methylation leads to an "unhappy mouse" which tends to be: Overweight, Diabetes prone, and Cancer prone.

Smoking and DNA Methylation

• Smoking results in large-scale reproducible changes to DNA methylation.

• These changes generally revert back towards normal after smoking cessation.

• Meta-analysis identified 2623 CpG sites (out of 18,760 CpG sites that were looked at).

• Reference: Joehanes et al, Circ Cardiovasc Genet. 2016

Smoking Effects on Children

• Similar effects are observed in children exposed in utero.

• AHRR (Aryl Hydrocarbon Receptor Repressor) is affected.

• Meta-analysis identified 568 CpG sites (out of 6073 CpG sites that were looked at?).

• Reference: Joubert et al, Am J Hum Genet. 2016

Smoking and Lung Cancer Prediction

• Prediction of lung cancer based on AHRR methylation levels shows a correlation between methylation and cancer risk.

• Observed 6-year cumulative incidence of lung cancer varies based on AHRR (cg05575921) methylation.

• Log-rank trend test: $p = 2 \times 10^{-7}$

• Reference: Bojesen et al, Thorax. 2017

Developmental Origins of Health and Disease (DOHaD)

Exposure to specific environments/diet early in life (or in utero) can lead to increased susceptibility to chronic disease later in life.

Dutch Hunger Winter

• 1944-45: Exposure to famine in utero during the Dutch Hunger Winter.

• Higher rates of obesity, diabetes, and heart disease were observed.

• Dependent on the exact timing of exposure:

  • First trimester: Associated with obesity, diabetes, heart disease, and schizophrenia.

  • Last trimester: Associated with smaller size but lower levels of obesity.

Dutch Hunger Winter - IGF2 Methylation

This information pertains to the Dutch Hunger Winter and its impact on $IGF2$ (Insulin-like Growth Factor 2) methylation. The graphs contrast early versus late exposure to famine conditions during gestation and its effect on methylation levels. Key observations focus on changes in methylation percentage relative to unexposed siblings.

• IGF2 Early: Shows methylation % differences between exposed and unexposed siblings. The time of ration is also displayed over time.

• IGF2 Late: Similar to the early exposure data, methylation differences are shown with rationed intake of food. Displaying methylation % differences between exposed and unexposed siblings. The ration is also displayed over time.

• Reference: Heijmans et al. PNAS 2008

Dutch Hunger Winter - Genome-Wide Study

• Genome-wide study of differences in methylation of siblings exposed to the Dutch Hunger Winter.

• 24 pairs assessed.

• 181 differentially methylated regions (DMRs) identified.

• Reference: Tobi et al. Nat Comm 2014

Dutch Hunger Winter - DNA Methylation Differences

• Graph (a) shows the average within-pair DNA methylation difference (%)

• Graph (b) displays the official government daily ration (kcal per day) and average temperature (°C)

• Specific genes like $CDH23$, $RFTN1$, $CPT1A$, $SMAD7$, $INSR$, and $KLF13$ are highlighted for their 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 - Illustration

• Diagram illustrating transgenerational inheritance, with "Son of Bob" as a placeholder.

Transgenerational Inheritance - Mechanism

• Exposure to an endocrine disruptor affects a gestating female (F0).

• This exposure impacts the germline of the F1 generation.

• The F2 generation is also affected.

• The F3 generation is the first unexposed generation, and any effects observed are considered transgenerational.

• Reference: Skinner 2016 Nat Rev Endocrin

Transgenerational Inheritance - Vinclozolin Exposure

• Exposure to Vinclozolin (F0) results in:

  • F3 generation exhibiting alterations in sperm motility.

  • These alterations are associated with changes in DNA methylation.

  • Some loci can escape early developmental re-programming.

• Reference: Skinner 2016 Nat Rev Endocrin

Behaviour

Licking and Grooming Behaviour in Rats

• Licking and grooming behaviour is part of normal mothering behaviour in rats.

• Rats vary in the extent of this behaviour.

• Licking and grooming behaviour is associated with reduced stress in adulthood.

• Associated with increased expression of GR (Glucocorticoid Receptor) in the hippocampus.

• Reference: Weaver et al, Nature Neuroscience 2004

Stress Response and Grooming

• Graph shows corticosterone levels (μg/dl) in response to stress.

• Vehicle: low-LG/ABN (licking and grooming/arched-back nursing)

• TSA: Trichostatin A

• Vehicle: high-LG/ABN

Methylation and Grooming - CpG Dinucleotide Analysis

• Graph (b) compares C-methylation (%) between Low-LG/ABN and High-LG/ABN groups across different CpG dinucleotide regions.

• NGFI-A (EGR1) binding region analyzed.

• Reference: Weaver et al, Nature Neuroscience 2004

Methylation and Grooming - Detailed Analysis

• Graph (d) provides a detailed analysis of C-methylation (%) at specific CpG dinucleotides.

• Comparison between L-L (Low-LG/ABN) and H-H (High-LG/ABN) groups.

• Reference: Weaver et al, Nature Neuroscience 2004

Stress Response and Grooming Repeated

• Corticosterone levels (μg/dl) in response to stress, comparing different groups.

Effect of Early Life Trauma - Humans

• Glucocorticoid receptor (GR) (NR3C1) methylation has been associated with depression.

• Early life events (child abuse) lead to increased risk of disease in adults.

• Potential role for FKBP5 (polymorphism in GR site associated with increased risk).

FKBP5 Methylation and Trauma

• Graph (b) shows FKBP5 methylation levels in individuals with and without trauma.

• FKBP5 rs1360780 polymorphism is considered.

• Similar effects observed in vitro with Dexamethasone.

• Reference: Klengel et al 2013, Nat Neuroscience

FKBP5 Post Cancer Treatment

• Childhood cancer treatment associated with increased chronic disease.

• Includes psychiatric illness.

• Early life trauma?

• Treatment with dexamethasone?

FKBP5 Methylation Post Cancer Treatment

• Graph shows FKBP5 methylation levels in controls, solid tumor patients, and ALL (acute lymphoblastic leukemia) patients.

Epigenetic Modifiers and Preventative Medicine

DNA Methylation and Aging

• "Young" DNA vs. "Old" DNA.

• Changes in CpG island methylation patterns with age.

DNA Methylation and Aging - Predictive Value

• Predicts “biological” and not chronological age.

• Predicts susceptibility to chronic disease.

• Predicts life expectancy.

• Reverse methylation and live longer?

Can Reversing Epigenetic Change Reverse Aging?

Reversing DNA Methylation and Aging

• The presenter hypothesizes that in terms of methylation, Aging, and Reversing Methylation may Reverse the Aging process.

Methylation Changes in B Cells

• Naive vs Memory B cells (Not class switched and Memory Class switched). Methylation affects the live years and proliferation of these groups.

• Reference: Oakes et al 2016

Methylation Changes in B Cells - Detailed Analysis

• Graph showing methylation changes in Naive vs CLL (Chronic Lymphocytic Leukemia) and Naive vs Memory B cells.

• Genes like FOXD3, ID4, DAPK1, and HOXA4 are highlighted.

• Reference: Oakes et al 2016

Methylation Changes in B Cells - Proliferation

• Alterations in DNA methylation can be related to proliferation.

• Not necessarily to loss of function.

• Increased aging = increased proliferation.

DNA Methylation - Chicken

• Methylation occurs mainly in Chicken.

HDAC - SIRT1 - Histone Deacetylases

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

SIRT1 / sir2 – C. elegans

• Graph shows the per cent alive over time in C. elegans with different genotypes (N2+ pRF4, geEx1, geEx2, geEx3).

• Reference: Tissenbaum & Guarente, Nature 2001

SIRT1/sir2 - Drosophila

• Graphs showing survivorship in Drosophila melanogaster with different conditions (Control 15% SY, 10 μM res 15% SY, 100 μM res 15% SY).

• Reference: Wood et al, Nature 2004

SIRT1/sir2 - Drosophila - Caloric Restriction

• Graphs showing Caloric restriction effects on survivorship in Drosophila melanogaster . The graphs include differen condition concentrations (Control 15% SY, 10 μM res 15% SY, 100 μM res 15% SY) and (Control 5% SY, 10 μM res 5% SY, 100 μM res 5% SY).

• Reference: Wood et al, Nature 2004

Caloric Restriction - Considerations

• Mood, Brain injury, Diabetes, Heart disease, Osteoperosis, Liver disease.

Caloric Restriction - SIRT1

• Caloric Restriction analysis regarding gene-expression and survivability.

Machado–Joseph Disease

• Also known as spinocerebellar ataxia type 3.

• Progressive cerebellar ataxia.

• Lack of muscle control and coordination of the upper and lower extremities.

Machado-Joseph Disease

• Graph (a) displays Cerebellar SIRT1 mRNA levels relative to WT (%).

• Comparison between WT, Tg MJD, Tg MJD + AL (ad libitum), and Tg MJD + CR (caloric restriction).

• Reference: Cunha-Santos et al, 2016 Nat. Commun.

Machado–Joseph Disease - SIRT1 and Clinical Trials

• SIRT1 levels rescued by CR.

• Significant improvement in symptoms.

• Can be replicated by genetic overexpression of SIRT1.

• Reference: Cunha-Santos et al, 2016 Nat. Commun.

• Resveratrol in phase 2 clinical trial for Friedreich Ataxia.

Epigenetics Summary

• Key epigenetic modifications:

  • DNA methylation

  • Histone modification

• Epigenetic mechanisms are heritable but labile.

• Epigenetic mechanisms can be influenced by a wide variety of exposures:

  • Diet

  • Toxins

  • Behaviour

Epigenetics Summary - Disease Modulation

• Epigenetic mechanisms can act as “sensors” that modulate the impact of diet/environment on chronic disease.

• Animal models demonstrate that genetic or pharmacological induced modulation of epigenetic mechanisms can alter susceptibility to age-related chronic disease.

• Can modulating the human epigenome prevent or reduce chronic disease in humans?

Lamarckian Renaissance?

Reference to Jean-Baptiste Lamarck.

Was Lamarck Right?

• Theory of Inheritance of Acquired Characteristics.

• Epigenetic mechanisms allow for the acquisition of characteristics based on environmental exposures.

• Not necessarily adaptive.

• Not generally transgenerational.

EpiGenetics

A final statement with Lamarck. A humorous conclusion to the lecture.