www.cmmt.ubc.ca

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

Understanding Epigenetics – a Journey Through Life

Developmental Epigenome Programming Environmental Influences on Epigenome

Same Genome – Many Epigenomes

Epigenetics refers to persistent and heritable alterations in genome information that do NOT involve changes in DNA sequence

From Genome to Epigenomes – Cellular Differentiation

>25000 Genes Identical Sequence 1 Genome

>200 Cell Types >200 Epigenomes

Persistent Programming Gene Expression Profiles

Active Gene -> mRNA made

“Epigenetic” Regulation of Gene Expression (Reversible!)

DNA Methylation, Chromatin, and Gene Regulation

Silent Gene -> no mRNA made

Unmethylated promoter DNA (CpG Islands) Methylated genic DNA Acetylated Histones Histone H3 K4 methylation Histone variant H3.3

Methylated promoter DNA (CpG Islands) Unmethylated genic DNA Deacetylated histones Histone H3 K9 methylation Canonical histone H3

Histone Modification Chromatin Remodeling Histone Variants RNA-Based Mechanisms DNA Methylation

Active Gene -> mRNA made

“Epigenetic” Regulation of Gene Expression (Reversible!)

DNA Methylation, Chromatin, and Gene Regulation

Silent Gene -> no mRNA made

Unmethylated promoter DNA (CpG Islands) Methylated genic DNA Acetylated Histones Histone H3 K4 methylation Histone variant H3.3

Methylated promoter DNA (CpG Islands) Unmethylated genic DNA Deacetylated histones Histone H3 K9 methylation Canonical histone H3

Histone Modification Chromatin Remodeling Histone Variants RNA-Based Mechanisms DNA Methylation

Maternal Diet Affects Epigenetic Gene Regulation in Isogenic Offspring (Avy /a)

Avy Expression

Avy DNA Methylation

High

High Low

Low

Maternal Methyl

High Low

Randy Jirtle Duke Waterland MCB 2003

Young Mice Adult Mice

Obese Lean

Nutrition and lifestyle of mother affects epigenome of child

Impact of Epigenetics on Health and Disease

Identical twins acquire discordant epigenomes during life-course

Maternal care affects epigenome of offspring

Environment

Epigenetics

Genetics

Phenotypic Variation

Integrative Model of Epigenetics

Environment

Epigenetics

Genetics

Phenotypic Variation

Integrative Model of Epigenetics

Do individuals vary in their DNA methylation pattern?

Extensive Epigenetic Variation in Human Tissues

What is DNA methylation associated with?

Demographic and Psychosocial Factors are Associated with DNA methylation.

Lam et al PNAS 2012

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

Presentation Outline

Early Life Socio-Economic Status Early Life Parental Stress Level

Early Life Experiences Getting Under the Skin

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)

Childhood Adulthood

Low SES Low SES High SES High SES

Low SES High SES Low SES High SES

Biological Residue of Low Early-Life Social Class

Miller et al PNAS 2009

DNA Methylation Correlated with Early Life Socio-Economic Status

Early Life SES (Age 1-5)

Current SES (Age 30-40)

Lam et al PNAS 2012

Maternal Warmth and Resilience of the Pro- Inflammatory Phenotype of Low Early-Life SES

0

2000

4000

6000

8000

10000

Low High

Maternal Warmth

IL-6

pro

duct

ion

(pg/

ml)

in

resp

onse

to T

LR2/

6 st

imul

atio

n

0

200

400

600

800

Low High

Maternal Warmth

IL-6

pro

duct

ion

(pg/

ml)

in

resp

onse

to T

LR9

stim

ulat

ion

Choose your parents wisely…. Chen et al Mol Psychiatry 2010

Paternal Stress

Paternal Stress

Maternal Stress

Maternal Stress Infancy

Preschool

Full Group (n=109)

Girls (n=60)

Boys (n=49)

139 HCS

HCS: FDR <5% MCS: FDR 5%-20%

1 HCS

3 HCS

3 HCS

3 HCS 29 MCS

6/9 HCS 314/1057 MCS

Epigenetic Vestiges of Early Parental Adversity Wisconsin Study of Families and Work (Longitudinal Birth Cohort)

Essex et al Child Development 2011

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%)

PGAM2 - cg23616741[P]

log(maternal stress at infancy)

avg

beta

0.2

0.3

0.4

0.5

0.6

0.2 0.4 0.6 0.8

PGAM2 - cg26057752[C]

log(maternal stress at infancy)

avg

beta

0.1

0.2

0.3

0.4

0.2 0.4 0.6 0.8

Maternal Stress During Infancy is Associated with DNA Methylation

Essex et al Child Development 2011

PKN1

maternal stress at infancy

avg

beta

0.6

0.7

0.8

0.9

0.2 0.4 0.6 0.8

C5orf21

maternal stress at infancy

avg

beta

0.6

0.7

0.8

0.9

0.2 0.4 0.6 0.8

Gender-Specific Association of Maternal Stress During Infancy with DNA Methylation

PKN1 rho=0.40 Δ6.4% q=0% rho=0.50 Δ7.5% q=0%

Maternal Stress Infancy Maternal Stress Infancy

Aver

age

beta

Aver

age

beta

C5orf21 rho=0.50 Δ10.6% q=0%

Associated CpG site in full group and boys

Female-specific associated CpG site

Essex et al Child Development 2011

Is variation in DNA methylation associated with children’s behavior?

Child-Centric Analysis of Wisconsin Family Data

Pre-School

Kindergarten

Grade 1

l9ans

bqN

orm

avg

beta

0.0

0.2

0.4

0.6

0.8

1.0

1 2 3 4 5 6 7

ALX4 rho= 0.404 C16orf30 rho= 0.408

1 2 3 4 5 6 7

C1orf188 rho= 0.442 C21orf56 rho= 0.323

1 2 3 4 5 6 7

C21orf56 rho= 0.368 CD24 rho= 0.447

DLX5 rho= 0.35 DLX5 rho= 0.371 DLX5 rho= 0.389 DLX5 rho= 0.398 FLJ11017 rho= 0.326

0.0

0.2

0.4

0.6

0.8

1.0FLJ20444 rho= 0.392

0.0

0.2

0.4

0.6

0.8

1.0LRRC2 rho= 0.399

1 2 3 4 5 6 7

POLR3C rho= 0.415 PRSS21 rho= 0.343

1 2 3 4 5 6 7

SLC29A4 rho= 0.455 TDGF1 rho= 0.346

1 2 3 4 5 6 7

TRIM16 rho= 0.382

l9@ans ↑246 (74) HCS 0.32 to 0.60 (0.32 to 0.48)

Grade 1 and Epigenetic Imprint Observed temperament; L9(PC;EL;LB) Anger scale

Boyce et al, in preparation

20: Temporal cortex 10: Frontal cortex 7: Parietal cortex

Korbinian Brodmann Areas

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

Presentation Outline

Gustavo Turecki, McGill University Michael Meaney, McGill University Eldon Emberly, Simon Fraser University

Tissue-Specific DNA Methylation Signatures in Human Brain and Blood

Farre et al, in preparation

Principal Components and Variance Distribution

PC1: Brain – Blood

Full Methylation

BR

AIN

P

BM

C

No Methylation

Meth450K Coord

Sam

ples

Tissue-Specific DNA Methylation of the Gene Encoding Glucocorticoid Receptor

PC4: Age, Brain only PC5: Age, Brain and Blood

Principal component reconstruction on an 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

DNA Methylation Signatures of Aging in Human Brain and Blood

Farre et al, in preparation

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

Epigenome

Tissue Specificity

Experiences Phenotypes

Genome

Development

Summary

Centre for Molecular Medicine and Therapeutics Dept. of Medical Genetics, CFRI, UBC Lucia Lam Sarah Neumann Sarah Mah Pau Farre

Human Early Learning Partnership National Institutes of Health Canadian Institutes of Health Research Mowafaghian Foundation Canadian Institute for Advanced Research

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

Acknowledgements

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

DNA Methylation and Gene Expression are not Tightly Linked Across Individuals

Lam et al PNAS 2012

Origin and consequences of variation of DNA methylation Hypothesis: recalling history and/or priming future response Interaction with other epigenetic modifications

Variation Correlated with: Demographic Factors, Biological Factors, Lifestyle, Immune Response, Early Life Experiences, and Genetics

Oligodeoxynucleotide TLR-9 agonist

Lipopolysaccharid TLR-4 agonist

DNA Methylation is Predictive of PBMC ex vivo Response.

Lam et al PNAS 2012

m67cbep

bqN

orm

avg

beta

0.0

0.2

0.4

0.6

3.5 4.0 4.5 5.0 5.5 6.0 6.5

ACTN2 rho= 0.395 ACTR3 rho= 0.325

3.5 4.0 4.5 5.0 5.5 6.0 6.5

C18orf22 rho= 0.33 DPYSL4 rho= 0.337

3.5 4.0 4.5 5.0 5.5 6.0 6.5

ELOVL6 rho= 0.339 HSD11B2 rho= 0.324

3.5 4.0 4.5 5.0 5.5 6.0 6.5

IGSF4 rho= 0.324

KLF2 rho= 0.361

3.5 4.0 4.5 5.0 5.5 6.0 6.5

LIX1 rho= 0.362 LOC126208 rho= 0.379

3.5 4.0 4.5 5.0 5.5 6.0 6.5

LR8 rho= 0.339 PDE2A rho= 0.324

3.5 4.0 4.5 5.0 5.5 6.0 6.5

SLC25A21 rho= 0.34

0.0

0.2

0.4

0.6

ZNF496 rho= 0.348

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)

Epigenetic Reflection of Pre-School Child Temperament

Anger component of Mother Reported "Children's Behavior Questionnaire"

Boyce et al, in preparation

INVtt88ex

bqN

orm

avg

beta

0.00.20.40.60.8

0.5 0.6 0.7 0.8 0.9 1.0

AMT rho= -0.27 C10orf89 rho= -0.262

0.5 0.6 0.7 0.8 0.9 1.0

C6orf25 rho= -0.28 CARD8 rho= -0.279

0.5 0.6 0.7 0.8 0.9 1.0

CHD1L rho= -0.295 DLX5 rho= -0.263

DLX5 rho= -0.268 DLX5 rho= -0.27 DLX5 rho= -0.312 ELAVL4 rho= -0.265 FIP1L1 rho= -0.291

0.00.20.40.60.8

GIMAP1 rho= -0.2760.00.20.40.60.8

GNAS rho= -0.265 IGF2AS rho= -0.396 KBTBD7 rho= -0.438 LRRFIP1 rho= -0.357 MGST1 rho= -0.275 MRGPRF rho= -0.274

MRGPRX1 rho= -0.359 NALP12 rho= -0.274 NPDC1 rho= -0.267 NR1I2 rho= -0.323 PRDM14 rho= -0.283

0.00.20.40.60.8

PRTN3 rho= -0.2760.00.20.40.60.8

RB1 rho= -0.276 TCP10 rho= -0.33 TRIM15 rho= -0.28 TRIM16 rho= -0.298 TRIM36 rho= -0.302 TSGA13 rho= -0.2620.00.20.40.60.8

ZMYND12 rho= -0.325

INVtt8@8ex ↓201(31) HCS -0.26 to -0.44 (-0.26 to -0.44)

Epigenetic Trace of Kindergarten Temperament EDI-like measures (teacher report); inverse TT8 Health and Behavior Questionnaire EXT (ODD;CD;OAG)

Boyce et al, in preparation