The document discusses epigenetics and how early life experiences can influence gene expression and health outcomes through epigenetic mechanisms. It provides three key points: 1) Early life socioeconomic status, parental stress levels, and childhood temperament can leave a "biological residue" in the form of epigenetic marks on DNA that influence gene expression and health. 2) Studies have found associations between early life adversity such as low socioeconomic status or high parental stress, and DNA methylation levels in adulthood. Certain genes show methylation changes correlated with early experiences. 3) Temperament and behavior in children has also been linked to DNA methylation levels, suggesting early life experiences can get "under

1. Epigenetic Embedding of
Early Life Experiences
Michael S. Kobor
Associate Professor
Centre for Molecular Medicine and Therapeutics
Child and Family Research Institute
Department of Medical Genetics
University of British Columbia
www.cmmt.ubc.ca

2. Understanding Epigenetics – a Journey Through Life
Epigenetics refers to persistent and heritable
alterations in genome information that do NOT
involve changes in DNA sequence
Same Genome – Many Epigenomes
Developmental Epigenome Programming
Environmental Influences on Epigenome

3. From Genome to Epigenomes –
Cellular Differentiation
>25000 Genes
Identical Sequence
1 Genome
Persistent Programming
Gene Expression Profiles
>200 Cell Types
>200 Epigenomes

4. DNA Methylation, Chromatin, and Gene Regulation
Histone Modification
Chromatin Remodeling
Histone Variants
RNA-Based Mechanisms
DNA Methylation
“Epigenetic” Regulation of Gene Expression (Reversible!)
Active Gene Silent Gene
-> mRNA made -> no mRNA made
Unmethylated promoter DNA Methylated promoter DNA
(CpG Islands) (CpG Islands)
Methylated genic DNA Unmethylated genic DNA
Acetylated Histones Deacetylated histones
Histone H3 K4 methylation Histone H3 K9 methylation
Histone variant H3.3 Canonical histone H3

5. DNA Methylation, Chromatin, and Gene Regulation
Histone Modification
Chromatin Remodeling
Histone Variants
RNA-Based Mechanisms
DNA Methylation
“Epigenetic” Regulation of Gene Expression (Reversible!)
Active Gene Silent Gene
-> mRNA made -> no mRNA made
Unmethylated promoter DNA Methylated promoter DNA
(CpG Islands) (CpG Islands)
Methylated genic DNA Unmethylated genic DNA
Acetylated Histones Deacetylated histones
Histone H3 K4 methylation Histone H3 K9 methylation
Histone variant H3.3 Canonical histone H3

6. Maternal Diet Affects Epigenetic Gene
Regulation in Isogenic Offspring (Avy /a)
Young Mice Adult Mice
Obese Lean
Low High Avy DNA Methylation
High Low Avy Expression
Low High Maternal Methyl
Randy Jirtle Duke
Waterland MCB 2003

7. Impact of Epigenetics on Health and Disease
Nutrition and lifestyle
of mother affects
epigenome of child
Maternal care affects epigenome
of offspring
Identical twins acquire discordant
epigenomes during life-course

8. Integrative Model of Epigenetics
Epigenetics
Phenotypic
Variation
Genetics Environment

9. Integrative Model of Epigenetics
Epigenetics
Phenotypic
Variation
Genetics Environment
Do individuals vary in their DNA methylation pattern?

10. Extensive Epigenetic Variation in Human Tissues
What is DNA methylation associated with?

11. Demographic and Psychosocial Factors are
Associated with DNA methylation.
Lam et al PNAS 2012

12. Presentation Outline
Epigenetics at the Interface of Genome and Environment
Epigenetic Variation in Adults
Biological Embedding of Early Life Experiences
Gene Expression and Pro-Inflammatory Phenotype
Epigenetic Vestiges of Family Environment
Epigenetic Reflections of Childhood Temperament
Turning Challenges into Opportunities – Peripheral versus Central

13. Early Life Experiences Getting Under the Skin
Early Life Socio-Economic Status Early Life Parental Stress Level
Childhood Temperament, Behavior, and Trajectories
Gregory Miller, Edith Chen (Psychology, UBC / Northwestern)
W. Thomas Boyce (Human Early Learning Partnership, UBC)
Clyde Hertzman (Human Early Learning Partnership, UBC)
Marilyn Essex (University of Wisconsin)

14. Biological Residue of Low Early-Life Social Class
Childhood Adulthood
Low SES Low SES
Low SES High SES
High SES Low SES
High SES High SES
Miller et al PNAS 2009

15. DNA Methylation Correlated with
Early Life Socio-Economic Status
Early Life SES Current SES
(Age 1-5) (Age 30-40)
Lam et al PNAS 2012

16. Maternal Warmth and Resilience of the Pro-
Inflammatory Phenotype of Low Early-Life SES
response to TLR2/6 stimulation
10000 800
response to TLR9 stimulation
IL-6 production (pg/ml) in
IL-6 production (pg/ml) in
8000
600
6000
400
4000
200
2000
0 0
Low High Low High
Maternal Warmth Maternal Warmth
Chen et al Mol Psychiatry 2010 Choose your parents wisely….

17. Epigenetic Vestiges of Early Parental Adversity
Wisconsin Study of Families and Work (Longitudinal Birth Cohort)
HCS: FDR <5%
Full Group Girls Boys
MCS: FDR 5%-20%
(n=109) (n=60) (n=49)
Maternal Stress 139 HCS 1 HCS 3 HCS
Infancy
Paternal Stress 3 HCS
Maternal Stress
Preschool
Paternal Stress 3 HCS 6/9 HCS
29 MCS 314/1057 MCS
Essex et al Child Development 2011

18. Maternal Stress During Infancy is
Associated with DNA Methylation
PGAM2 - cg23616741[P] PGAM2 - cg26057752[C]
0.6
0.4
0.5
0.3
avg beta
avg beta
0.4
0.2
0.3
0.1
0.2
0.2 0.4 0.6 0.8 0.2 0.4 0.6 0.8
log(maternal stress at infancy) log(maternal stress at infancy)
In the set of 37 high confidence sites associated with maternal stress at infancy and
having more than 5% change in DNA, two CpG loci belonged to the same gene, PGAM2,
which encodes phosphoglycerate mutase 2.
cg26057752 CpG site (rho = .31, 9.6% DNA methylation change, FDR = 0%)
cg23616741 CpG site (rho = .25, 10.4% DNA methylation change, FDR = 0%)
Essex et al Child Development 2011

19. Gender-Specific Association of Maternal Stress
During Infancy with DNA Methylation
Associated CpG site in Female-specific
full group and boys
PKN1
associated CpG site
C5orf21
0.9 0.9
Average beta
beta
0.8 0.8
Averagebeta
avg beta
avg
0.7 0.7
0.6 0.6
PKN1 rho=0.40 Δ6.4% q=0% C5orf21 rho=0.50 Δ10.6% q=0%
rho=0.50 Δ7.5% q=0%
0.2 0.4 0.6 0.8 0.2 0.4 0.6 0.8
Maternal Stress Infancy
maternal stress at infancy Maternal Stress Infancy
maternal stress at infancy
Is variation in DNA methylation associated with children’s behavior?
Essex et al Child Development 2011

20. Child-Centric Analysis of Wisconsin Family Data
Pre-School
Kindergarten
Grade 1

21. Grade 1 and Epigenetic Imprint
Observed temperament; L9(PC;EL;LB) Anger scale
l9@ans ↑246 (74) HCS 0.32 to 0.60 (0.32 to 0.48)
1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7
LRRC2 rho= 0.399 POLR3C rho= 0.415 PRSS21 rho= 0.343 SLC29A4 rho= 0.455 TDGF1 rho= 0.346 TRIM16 rho= 0.382
1.0
0.8
0.6
0.4
0.2
0.0
DLX5 rho= 0.35 DLX5 rho= 0.371 DLX5 rho= 0.389 DLX5 rho= 0.398 FLJ11017 rho= 0.326 FLJ20444 rho= 0.392
1.0
bqNorm avgbeta
0.8
0.6
0.4
0.2
0.0
ALX4 rho= 0.404 C16orf30 rho= 0.408 C1orf188 rho= 0.442 C21orf56 rho= 0.323 C21orf56 rho= 0.368 CD24 rho= 0.447
1.0
0.8
0.6
0.4
0.2
0.0
1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7
l9ans
Boyce et al, in preparation

22. Presentation Outline
Epigenetics at the Interface of Genome and Environment
Epigenetic Variation in Adults
Biological Embedding of Early Life Experiences
Turning Challenges into Opportunities – Peripheral versus Central
Korbinian Brodmann Areas
7: Parietal cortex 10: Frontal cortex 20: Temporal cortex
Gustavo Turecki, McGill University
Michael Meaney, McGill University
Eldon Emberly, Simon Fraser University

23. Tissue-Specific DNA Methylation
Signatures in Human Brain and Blood
Principal Components
and Variance Distribution
PC1: Brain – Blood
Farre et al, in preparation

24. Tissue-Specific DNA Methylation of the
Gene Encoding Glucocorticoid Receptor Full
Methylation
PBMC
Samples
BRAIN
No
Methylation
Meth450K Coord

25. DNA Methylation Signatures of Aging
in Human Brain and Blood
PC4: Age, Brain only Principal component reconstruction on an
PC5: Age, Brain and Blood Independent dataset composed of blood
Samples of 656 individuals:
(A) PC4: correlation 0.104 with p-value: 0.526.
(B) PC5: correlation 0.554 with p-value: 1.081E-51
Farre et al, in preparation

26. Summary
Epigenetics as an Integral Component of Human Health and Disease
Epigenetic Variation in Adults
Tissue-Specific Variation Associated with Many Variables
Genomic Embedding of Early Life Experiences
Biological Residue of Early Life Poverty
DNA Methylation Associated with Early Life Parental Stress
Childhood Temperament is Correlated with DNA Methylation
Peripheral versus Central Tissues
Complex Distinct and Overlapping Signatures

27. Summary
Epigenome
Experiences Phenotypes
Tissue
Specificity
Development
Genome

28. Acknowledgements
Centre for Molecular Medicine and Therapeutics
Dept. of Medical Genetics, CFRI, UBC
Lucia Lam
Sarah Neumann
Sarah Mah
Pau Farre
Edith Chen University of British Columbia / Northwestern University
Greg Miller University of British Columbia / Northwestern University
W. Thomas Boyce University of British Columbia
Clyde Hertzman University of British Columbia
Marilyn Essex University of Wisconsin
Hunter Fraser Stanford University
Eldon Emberly Simon Fraser University
Gustavo Turecki McGill University
Michael Meaney McGill University
Human Early Learning Partnership
National Institutes of Health
Canadian Institutes of Health Research
Mowafaghian Foundation
Canadian Institute for Advanced Research

29. Issues to Consider
Correlation versus Causality
Robustness of DNA Methylation in Response to Environments
Malleability of Marks upon Intervention
Tissue Specificity – Peripheral versus Central
Relationship between DNA Methylation and Gene Expression
Interplay between Genetics, Epigenetics and the Environment
Application of Different Statistical Approaches
Turning Challenges into Opportunities: the Next 5 Years
Epigenetics – is it Part of “the Missing Heritability”?
What is the Role of Epigenetics in Common Diseases?
Does Epigenetic Serve as a Memory of the Past, Predicting Future Response?
Disease-Oriented Cohorts, Longitudinal Patient Samples
Birth Cohorts, Environmental Assessments
Predictive Epigenetic Biomarkers
Causality: Model Organisms, Therapeutic Intervention
Expanding Beyond DNA Methylation (non-coding RNAs, Histones)
Drug Effects on Epigenome

30. DNA Methylation and Gene Expression are
not Tightly Linked Across Individuals
Origin and consequences of variation of DNA methylation
Hypothesis: recalling history and/or priming future response
Interaction with other epigenetic modifications
Lam et al PNAS 2012

31. DNA Methylation is Predictive of
PBMC ex vivo Response.
Oligodeoxynucleotide Lipopolysaccharid
TLR-9 agonist TLR-4 agonist
Variation Correlated with:
Demographic Factors, Biological Factors, Lifestyle, Immune Response,
Early Life Experiences, and Genetics
Lam et al PNAS 2012

32. Epigenetic Reflection of Pre-School
Child Temperament
Anger component of Mother Reported
"Children's Behavior Questionnaire"
M67cb@an ↑8(2) HCS 0.36 to 0.39 (0.36 to 0.38)
↑26(7) MCS 0.30 to 0.35 (0.30 to 0.33)
3.5 4.0 4.5 5.0 5.5 6.0 6.5 3.5 4.0 4.5 5.0 5.5 6.0 6.5 3.5 4.0 4.5 5.0 5.5 6.0 6.5
KLF2 rho= 0.361 LIX1 rho= 0.362 LOC126208 rho= 0.379 LR8 rho= 0.339 PDE2A rho= 0.324 SLC25A21 rho= 0.34 ZNF496 rho= 0.348
0.6
0.4
bqNorm avgbeta
0.2
0.0
ACTN2 rho= 0.395 ACTR3 rho= 0.325 C18orf22 rho= 0.33 DPYSL4 rho= 0.337 ELOVL6 rho= 0.339 HSD11B2 rho= 0.324 IGSF4 rho= 0.324
0.6
0.4
0.2
0.0
3.5 4.0 4.5 5.0 5.5 6.0 6.5 3.5 4.0 4.5 5.0 5.5 6.0 6.5 3.5 4.0 4.5 5.0 5.5 6.0 6.5 3.5 4.0 4.5 5.0 5.5 6.0 6.5
m67cbep
Boyce et al, in preparation

33. Epigenetic Trace of Kindergarten Temperament
EDI-like measures (teacher report);
ZMYND12 rho= -0.325 TT8 Health and Behavior Questionnaire EXT (ODD;CD;OAG)
inverse
0.8
0.6
INVtt8@8ex 0.4 ↓201(31) HCS -0.26 to -0.44 (-0.26 to -0.44)
0.2
0.0
RB1 rho= -0.276 TCP10 rho= -0.33 TRIM15 rho= -0.28 TRIM16 rho= -0.298 TRIM36 rho= -0.302 TSGA13 rho= -0.262
0.8
0.6
0.4
0.2
0.0
MRGPRX1 rho= -0.359 NALP12 rho= -0.274 NPDC1 rho= -0.267 NR1I2 rho= -0.323 PRDM14 rho= -0.283 PRTN3 rho= -0.276
0.8
0.6
bqNorm avgbeta
0.4
0.2
0.0
GNAS rho= -0.265 IGF2AS rho= -0.396 KBTBD7 rho= -0.438 LRRFIP1 rho= -0.357 MGST1 rho= -0.275 MRGPRF rho= -0.274
0.8
0.6
0.4
0.2
0.0
DLX5 rho= -0.268 DLX5 rho= -0.27 DLX5 rho= -0.312 ELAVL4 rho= -0.265 FIP1L1 rho= -0.291 GIMAP1 rho= -0.276
0.8
0.6
0.4
0.2
0.0
AMT rho= -0.27 C10orf89 rho= -0.262 C6orf25 rho= -0.28 CARD8 rho= -0.279 CHD1L rho= -0.295 DLX5 rho= -0.263
0.8
0.6
0.4
0.2
0.0
0.5 0.6 0.7 0.8 0.9 1.0 0.5 0.6 0.7 0.8 0.9 1.0 0.5 0.6 0.7 0.8 0.9 1.0
INVtt88ex
Boyce et al, in preparation