Epigenetics Asthma Denmark Koppelman 2014 ... · • Role of DNA methylation in astma. T cell differentiation Gene Mechanism IL4 Demethylation of GATA4 binding site Demethylation

Epigenetics of asthma

Groningen Research Institute of Asthma and COPD

Gerard KoppelmanGerard KoppelmanGerard KoppelmanGerard Koppelman


Pediatric Pulmonology and Pediatric Allergology

Beatrix Children’s Hospital, University Medical Center Groningen

Epigenetics of asthma


Gerard KoppelmanGerard KoppelmanGerard KoppelmanGerard Koppelman


Pediatric Pulmonology and Pediatric Allergology

Beatrix Children’s Hospital, University Medical Center Groningen

This presentation

• From genetics to epigenetics?

• The promise of epigenetics

• What do we know so far?

• Novel insights in the epigenetics of asthma

This presentation

From genetics to epigenetics?

The promise of epigenetics

What do we know so far?

Novel insights in the epigenetics of asthma

Genetic variation

DNA3 billion basepairs

gene

Single nucleotide polymorphisms

About 90% of all human genetic variation

SNPs

30,000 genes

Genetic variation

ACCGTTCGGG

Single nucleotide polymorphisms

About 90% of all human genetic variation

From genetics to epigenetics

mRNA

DNA - Genetic variation

mRNA

Asthma

Protein


Genetic assocation study

• Method: case

Reference allele

Genetic assocation study

control

Risk allele

Genetics (status 2012)Genetics (status 2012)

Contribution of genetics to understanding disease

• Mendelian disease• Complex disease

variants from 165 diseases

How much of heritability explained?• Type 1 diabetes• Crohn’s disease• Asthma

Contribution of genetics to understanding disease

2000 2010

<100 2.85012 1.100

variants from 165 diseases

How much of heritability explained?60 %20-25%< 5 % Lander ES, Nature 2010

GWAS of the GABRIEL consortium

/IL1RL1

GWAS of the GABRIEL consortium

Moffatt et al, NEJM 2010; 363: 13

Asthma risk loci overlap in EVE and Gabriel

Gene/Region EVE17q21(ORMDL3/GSDML)

1.2x10-14

IL1RL1/IL18R1 (chr. 2) 1.4x10-8

TSLP (chr. 5) 7.3x10-10

IL33 (chr. 9) 2.5x10-7IL33 (chr. 9) 2.5x10-7

PYHIN1 (chr. 1) 3.6x10-7

HLA-DQ (chr. 6) 0.014SMAD3 (chr. 15) 1.9x10-4

IL2RB (chr. 22) nsSLC22A5 (chr. 5) nsIL13 (chr. 5) nsRORA (chr. 15) 2.1x10-3

*childhood asthmaThe EVE Consortium – C. Ober

Asthma risk loci overlap in EVE and Gabriel

GABRIEL Race/Ethnicity

6.4x10-23* All

3.4x10-9 All7.5-8 All

9.2x10-10 All9.2x10-10 All-- African Ancestry

7.0x10-14 All3.9x10-9 Eur/EurAmer1.1x10-8 Europeans2.2x10-7 Europeans1.4x10-7 Europeans1.1x10-7 Eur/EurAmer

*childhood asthma

What have we learnt?

• Multiple SNPs, small effects, so far explains less than 5 % of asthma

• Asthma heterogeneity has genetic basis• Asthma heterogeneity has genetic basis– Ethnic specific

• PYHIN1 (Pyrin and HIN domain family member 1interferon inducible nuclear factor 1

• Susceptibility SNPs in Afr Am are not present in subjects of European descent

– Phenotype specific • PDE4D as Asthma + Bronchial hyperresponsiveness gene• 17q21 confers susceptibility to childhood onset asthma

What have we learnt?

Multiple SNPs, small effects, so far explains less

Asthma heterogeneity has genetic basisAsthma heterogeneity has genetic basis

PYHIN1 (Pyrin and HIN domain family member 1, aka interferon inducible nuclear factor 1) is specific to Afr Am. Susceptibility SNPs in Afr Am are not present in subjects of

Phenotype specific as Asthma + Bronchial hyperresponsiveness gene

17q21 confers susceptibility to childhood onset asthma

Chr 17q21 SNPs and asthma onset

Age at onset asthma

Chr 17q21 SNPs and asthma onset

Bouzigon et al NEJM 2008

Age at onset asthma


mRNA

Genetic variationCpG

MiRNA

Small non coding RNAmRNA

Asthma

Protein

Small non coding RNA

Histone modification

Chromatin remodelling


CpG-M DNA methylation

MiRNA

Small non coding RNA Micro RNAsSmall non coding RNA


Chromatin remodellingRegulation of

DNA transcription

Epigenetics

• Heritable ? changes in gene expression that occur without directly changing the DNA sequencesequence

• Why? Adaptation to the environment, organ development, role in disease

Epigenetics

Heritable ? changes in gene expression that occur without directly changing the DNA

Why? Adaptation to the environment, organ development, role in disease

DNA Methylation

• Cytosine -> 5’-Methylcytosine

• CpG Islands (1-4 kB)

• CpG Islands in • CpG Islands in promoters and at transcription start sites (75 – 88%)

DNA Methylation

Kabesch et al, ERJ 2010

Methylation: DNA methyltransferases add

methylgroup to cytosine

MMMMMM

CpG island

Methylated

M

Methylated

Not methylated

Small differences in methylation (~15%)(~40%) in gene transcription Oates et al. (2006)

Methylation: DNA methyltransferases add

methylgroup to cytosine

Gene

SuppressedSuppressed

Active

(~15%) can result in large differences Oates et al. (2006) Am J Hum Genet 79: 155

How many different basepairs are there?

• A, C, G, T• 5 mC (5 methyl cytosine)• 5 hmC (5 hydroxy methyl cytosine)• 5 hmC (5 hydroxy methyl cytosine)

How many different basepairs are there?

5 mC (5 methyl cytosine)5 hmC (5 hydroxy methyl cytosine)5 hmC (5 hydroxy methyl cytosine)


Eu-chromatin

Hetero-chromatin


Ummethylation of CpG,

acetylation of histones:


histones:

EXPRESSION

Methylation of CpG and histones:

NO EXPRESSION

DNA Methylation and histone modifications

regulate gene expression

Kabesch and Adcock Biochimie 94 (2012) 2231 e2241

DNA Methylation and histone modifications

regulate gene expression

Kabesch and Adcock Biochimie 94 (2012) 2231 e2241

The synthesis and processing of microRNA

POL II

C T D

TFIIE

TFIID Complex

TAF II130 TAF II250

TBPTAF II31

TAF II80

TAF II20

TFIIF

TFIIH

Kin28

TFIIBTFIIA

RNaseIII(Drosha)

Transcription

Dicer

Argonaute 2(RNase H)

m7G

(Drosha)

TRBP

Capping, splicingand polyadenylation

mRNA degradation

Translation inhibition

The synthesis and processing of microRNA

RNase IIIRNase

(Drosha)

Pasha

RNaseIII

Pasha

Nucleus

Dicer

Argonaute 2(RNase H)

Dicer

AAAA

(Drosha) III(Drosha)

TRBP

Exportin 5

Ran

TRBP

What increases with more complex organisms (homo sapiens) (when

compared to bacteria, yeast)?

• The number of chromosomes?• The number of chromosomes?

• The number of base pairs?

• The number of genes?

• The percentage of non-coding DNA?

What increases with more complex organisms (homo sapiens) (when

compared to bacteria, yeast)?

The number of chromosomes?The number of chromosomes?

The number of base pairs?

coding DNA?

What correlates with more complex organisms (homo sapiens)?






This presentation

• What is epigenetics?




This presentation




The promise of epigenetics of asthma

• Epigenetics may explain– Effect of the environment during critical time window

“programming”– Differences in end organ expression (tissue specific

effects) effects) – Changes in phenotypes over time– Transgenerational effects– Parent of offspring effects

Koppelman and Nawijn, Curr Opin Allergy & Clin Immunology 2011: 11 (5) 414

The promise of epigenetics of asthma

Epigenetics may explainEffect of the environment during critical time window

Differences in end organ expression (tissue specific

Changes in phenotypes over timeTransgenerational effectsParent of offspring effects

Koppelman and Nawijn, Curr Opin Allergy & Clin Immunology 2011: 11 (5) 414–419

Environmental factors may induce epigenetic effects

Environmental factors may induce epigenetic effects

Miller and Ho, AJRCCM 2008

Transgenerational effects of ETS exposure on asthma



• Risk of ETS exposure may be transmitted across two generationsacross two generations

• N = 338 children with asthma, age 5 • N = 570 controls, matched for in utero smoking• Risk of asthma – depending on smoking of

grandmother and / or mother


Risk of ETS exposure may be transmitted

N = 338 children with asthma, age 5 N = 570 controls, matched for in utero smoking

depending on smoking of grandmother and / or mother

Li et al, Chest 2005


I

II

III


grandchild


• Risk of asthma in grandchild

– Grandmaternal smoking– Grandmaternal smoking(independent from maternal smoking)

– Grandmaternal and maternal smoking

– This could be explained by epigenetics, but this remains to be shown!


Risk of asthma in grandchild

Grandmaternal smoking OR 1.8 [1.0 – 3.3]Grandmaternal smoking OR 1.8 [1.0 – 3.3](independent from maternal smoking)Grandmaternal and maternal smoking

OR 2.6 [1.6 – 4.5]This could be explained by epigenetics, but this

Li et al, Chest 2005



Grandmother exposes

- Daughter - Daughter

- Granddaughter

(in females, oogenesis starts in utero)

Maternal effects in asthma

• Risk of asthma higher in children of mother with asthma, compared to fathers with athma

• Example: • Example: – 200 consecutive cases of childhood asthma, – Approximately twice as many children had atopic

mothers than atopic fathers (Bray, J Allergy, 1931)• Could epigenetic inheritance be gender specific?


Risk of asthma higher in children of mother with asthma, compared to fathers with athma

200 consecutive cases of childhood asthma, Approximately twice as many children had atopic mothers than atopic fathers (Bray, J Allergy, 1931)

Could epigenetic inheritance be gender specific?


• Several studies show differences in methylation patterns depending on paternal or maternal origin of the alleleles (imprinting, X chromosome origin of the alleleles (imprinting, X chromosome inactivation)

• No positive studies so far link this to asthma


Several studies show differences in methylation patterns depending on paternal or maternal origin of the alleleles (imprinting, X chromosome origin of the alleleles (imprinting, X chromosome

No positive studies so far link this to asthma

This presentation





This presentation




What do we know so far ?

• Literature review 2013 on epigenetics and asthma

• Keywords : asthma, allergy, methylation, epigenetics

• Comparison of reviews versus original research

• Genome wide versus candidate gene studies

DeVries and Vercelli Asian Pac J All Immunol 2013:31:183


Literature review 2013 on epigenetics and

Keywords : asthma, allergy, methylation,

Comparison of reviews versus original

Genome wide versus candidate gene studies

DeVries and Vercelli Asian Pac J All Immunol 2013:31:183-9


Comparison reviews versus original data

40

Number of manuscripts until 2013 Number of manuscripts until 2013 Number of manuscripts until 2013 Number of manuscripts until 2013


0

10

20

30

Reviews Original research

31


Comparison reviews versus original dataNumber of manuscripts until 2013 Number of manuscripts until 2013 Number of manuscripts until 2013 Number of manuscripts until 2013

DeVries and Vercelli Asian Pac J All Immunol 2013:31:183-9Original research

25

Number

What do we know so far ?• Genome wide versus candidate gene studies

15

Number Number Number Number


0

5

10

Genome wide Candidate genes

7

What do we know so far ?Genome wide versus candidate gene studies

Number Number Number Number

DeVries and Vercelli Asian Pac J All Immunol 2013:31:183-9Candidate genes

14 Number


• Role of methylation in allergy (Th1/Th2 skewing)

• Environmental effects on the DNA methylome• Tissue specific effects explained by

methylation• Role of DNA methylation in astma


Role of methylation in allergy (Th1/Th2

Environmental effects on the DNA methylomeTissue specific effects explained by

Role of DNA methylation in astma

T cell differentiation

Gene MechanismIL4 Demethylation of GATA4 binding site

Demethylation of the 5’ flanking region of the IL4 promoterDemethylation of the 5’ flanking region of the IL4 promoterIncrease in histone acetylation

IFNG Methylation of AP1 binding site in promoterIL13, IL5 Increase in histone acetylation

This leads to Th2 deviationThis leads to Th2 deviationThis leads to Th2 deviationThis leads to Th2 deviation

T cell differentiation

Demethylation of GATA4 binding siteDemethylation of the 5’ flanking region of Demethylation of the 5’ flanking region of

Increase in histone acetylationMethylation of AP1 binding site in promoterIncrease in histone acetylation

S-M Ho, JACI 2010:126: 453-65

This leads to Th2 deviationThis leads to Th2 deviationThis leads to Th2 deviationThis leads to Th2 deviation

Epigenetics in T cell differentiation


Epigenetics in T cell differentiation

S-M Ho, JACI 2010:126: 453-65Kabesch et al, ERJ 2010

Effects of farming

– PASTURE study: rural birth cohort– DNA from cord blood and whole blood age 4,5 y– 46 samples– 10 candidate genes, including

IL13, IL4, STAT6, RUNX3, FOXP3, CHI3LIIL13, IL4, STAT6, RUNX3, FOXP3, CHI3LI– Questions:

– Change over time?– Effect of farm?– Relation with asthma?

Effects of farming

PASTURE study: rural birth cohortDNA from cord blood and whole blood age 4,5 y

10 candidate genes, including ORMDL3, RAD50, IL13, IL4, STAT6, RUNX3, FOXP3, CHI3LIIL13, IL4, STAT6, RUNX3, FOXP3, CHI3LI

Relation with asthma?

Michel et al, Allergy, 2013; 68 : 355-64

Effects of farming– PASTURE study– DNA from cord blood and – 46 samples– 10 candidate genes, including

IL13,IL4, STAT6, RUNX3, FOXP3, CHI3LIIL13,IL4, STAT6, RUNX3, FOXP3, CHI3LI– Questions:

– Change over time?– Effect farm?– Relation asthma?

Effects of farming

and whole blood age 4,5 y

including ORMDL3, RAD50, IL13,IL4, STAT6, RUNX3, FOXP3, CHI3LIIL13,IL4, STAT6, RUNX3, FOXP3, CHI3LI

IL4


Effects of farming

Results– Effect of farming on

STAT6, IL13, RAD50

– Effect of timing: 15 gene

– Asthma: one gene regionAsthma87.9

Michel et al, Allergy, 2013; 68 : 355

Effects of farming

4 genes (ORMDL1, STAT6, IL13, RAD50)

Effect of timing: 15 gene regions

region ORMDL3 Asthma Control87.9 85.8 p=0.03


Effects of materal smoking

Norwegian Mother and Child– DNA from cord blood– 1,062 samples– Smoking assessed by– Smoking assessed by

mothers– Epigenome wide analysis– Replication study in 36 samples

Joubert et al, Env Health Perspectives, 120 (10): 1425


Child Cohort Studyblood

by plasma cotinine in by plasma cotinine in

analysis using Illumina 450 Kin 36 samples from US

Joubert et al, Env Health Perspectives, 120 (10): 1425-31






- 26 CpG sites in 10 genes associated with maternal smoking

- AHRR (aryl hydrocarbon receptor repressor gene ) CYP1A1 and GFI1 replicatedCYP1A1 and GFI1 replicated

- Average methylation difference: 3- Biological plausible pathway: detoxification of cigarette

smoke components



26 CpG sites in 10 genes associated with maternal

aryl hydrocarbon receptor repressor gene ) , replicatedreplicated

Average methylation difference: 3-10% Biological plausible pathway: detoxification of cigarette


Effects of active smoking

- German KORA study- 1793 participants- Several EWAS hits, Including AHRRIncluding AHRRMethylation patterns of Former smokers more Like never smokers

Zeilinger et al, PLOS ONE 2013

Effects of active smoking

Zeilinger et al, PLOS ONE 2013

Environmental factors linked to asthma may induce epigenetic effects

• Folic acid (mouse) Hollingsworth, J Clin Invest. 2008;118(10):3462

• Plasma homocysteine, birth weight2011 6:1,86

• Maternal smoking Breton et al, AJRCCM 2009.1;180(5):462• Maternal smoking Breton et al, AJRCCM 2009.1;180(5):462

• Air pollution Perera et al, PLOS ONE 2009; 4(2): e4488)

• Maternal Stress Chen et al, AJRCCM 2013 (187): 584

– Important in asthma development?

Environmental factors linked to asthma may induce epigenetic effects

Hollingsworth, J Clin Invest. 2008;118(10):3462-9

Plasma homocysteine, birth weight Fryer et al, Epigenetics 2011 6:1,86-94

Breton et al, AJRCCM 2009.1;180(5):462-7.Breton et al, AJRCCM 2009.1;180(5):462-7.

Perera et al, PLOS ONE 2009; 4(2): e4488)

Chen et al, AJRCCM 2013 (187): 584-8

Important in asthma development?

Tissue specific effects on

Asthma

Asthma + BHR

Asthma and Total IgE

Asthma and specific IgE

Tissue specific effects on ADAM 33

Van Eerdewegh et al., Nature 2002

ADAM33 was the first asthma gene found by positional cloning

A D G J MC F I L NKHEB

A Disintegrin And Metalloprotease (

ADAM33, ADAM33, ADAM33, ADAM33, a gene for asthma and BHRa gene for asthma and BHRa gene for asthma and BHRa gene for asthma and BHR

A-VT-AY-H

proteolysis adhesion

Zn2+

site

activation

Expression of ADAM33 mRNA restricted to mesenchymal cells ; smooth muscle, fibroblasts & myofibroblasts

CpG CpG CpG CpG

P S VO R UTQ

etalloprotease ( ADAM)33

a gene for asthma and BHRa gene for asthma and BHRa gene for asthma and BHRa gene for asthma and BHR

adhesion fusion signalling

3’ UTR

Promotes efficient maturaton of ADAM33

Expression of ADAM33 mRNA restricted to mesenchymal cells ; smooth muscle, fibroblasts & myofibroblasts

Epigenetic effects are tissue specific

• ADAM33 mRNA is expressed in fibroblasts, but not in epithelial cells

Epithelial cells

Yang et al, JACI 2008; 121

Epithelial cells


ADAM33 mRNA is expressed in fibroblasts, but not in epithelial cells

fibroblasts

Yang et al, JACI 2008; 121-1393-9

ADAM33

GAPDH

fibroblasts


• ADAM33 gene is methylated in epithelial cells, but not in fibroblasts

Epithelial cells,


Epithelial cells, n=3

Fibroblasts, n=3


ADAM33 gene is methylated in epithelial cells, but not in fibroblasts

Yang et al, JACI 2008; 121-1393-9


• Demethylation of CpG Islands of ADAM33 induces mRNA expression in epithelial cells



Demethylation of CpG Islands of ADAM33 induces mRNA expression in epithelial cells

Yang et al, JACI 2008; 121-1393-9


• Micro RNAs are regulatory small non coding RNAs• At least 700 miRNAs described• Micro RNA targets 3’UTR sequences of on average

100 genes

• Aims: – Role in asthma? – Effect of inhaled corticosteroids? – Tissue specific effects?

Williams et al, PLOS ONE 2009 4(6): e5889


Micro RNAs are regulatory small non coding RNAsAt least 700 miRNAs describedMicro RNA targets 3’UTR sequences of on average

Effect of inhaled corticosteroids?


Micro RNAs in asthma?

• Airway wall biopsies of 8 patients with mild asthma, and 8 controls

• 227 miRNAs investigated in airway wall biopsies

• 227 miRNAs investigated in airway wall biopsies


Micro RNAs in asthma?

Airway wall biopsies of 8 patients with mild asthma, and 8 controls227 miRNAs investigated in airway wall 227 miRNAs investigated in airway wall


No differences in micro RNA expression asthma vs healthy controls


No differences in micro RNA expression asthma vs healthy controls


Tissue specific expression of micro RNAs

Differences in micro RNA expression between epithelial cells, smooth muscle cells, alveolar macrophages


Targets suggest role in Important cellular processes in the lung

Tissue specific expression of micro RNAs

Differences in micro RNA expression between epithelial cells, smooth muscle cells, alveolar


Important cellular processes

Integration: Environment (E), methylation and asthma

- Model 1: Environmental effect is methylation mediated- E � Methylation � Disease

- Model 2: Reverse Causality- E � Disease, Disease �

- Model 3: Independent (Common causes)- E � Methylation- E � Disease

Integration: Environment (E), methylation and asthma

: Environmental effect is methylation

Disease

: Reverse Causality� Methylation

: Independent (Common causes)

After Liu et al, Nat Biotech 2013 (31): 142-7

Air Pollution, methylation and asthma

• Inner city cohort of 700 Children in New York• Asthma prevalence 25 % !• Role of transplacental exposure to airborne

polycyclic aromatic hydrocarbonspolycyclic aromatic hydrocarbons

• Aim– DNA methylation of cord blood cells– Transplacental exposure to PAH – Childhood asthma

Perera et al, PLOS ONE 2009; 4(2): e4488


Inner city cohort of 700 Children in New YorkAsthma prevalence 25 % !Role of transplacental exposure to airborne polycyclic aromatic hydrocarbonspolycyclic aromatic hydrocarbons

DNA methylation of cord blood cellsTransplacental exposure to PAH



• N = 20 children from New York cohort• Methylation sensitive restriction fingerprinting

of cord white blood cells• 31 loci were related to maternal PAH exposure• 31 loci were related to maternal PAH exposure• Of these, 6 genes with known CpG Island

– One gene whose methylation status correlated with best with gene expression:

(Acyl co-A synthethase long



N = 20 children from New York cohortMethylation sensitive restriction fingerprinting of cord white blood cells31 loci were related to maternal PAH exposure31 loci were related to maternal PAH exposureOf these, 6 genes with known CpG Island

One gene whose methylation status correlated with best with gene expression: ACSL3

A synthethase long-chain family member 3)



**


N= 56 children


*



• Comments

– Small pilot study– Incomplete coverage of the genome by initial assay– Incomplete coverage of the genome by initial assay– Needs replication

– Is one of the first study linking prenatal exposure, methylation patterns and asthma at age 5.



Incomplete coverage of the genome by initial assayIncomplete coverage of the genome by initial assay

Is one of the first study linking prenatal exposure, methylation patterns and asthma at age 5.


Methylation and wheezing

- INMA project (Menorca and Sabadell)- Whole blood DNA at age 4- Wheezing phenotypes at age 4

- Stage 1: 27K Methylation array in 141 children - Stage 1: 27K Methylation array in 141 children from INMA Menorca - 61 never / 41 transient wheezing- 3 late onset / 17 persistent wheezing

- Stage 2: Replication in INMA Sabadell - Assessment of relation SNPs


INMA project (Menorca and Sabadell)Whole blood DNA at age 4Wheezing phenotypes at age 4-6 y

Stage 1: 27K Methylation array in 141 children Stage 1: 27K Methylation array in 141 children

61 never / 41 transient wheezing3 late onset / 17 persistent wheezing

Stage 2: Replication in INMA Sabadell Assessment of relation SNPs - methylation

Morales et al, AJRCCM 2012 (185): 937-43


Gene Chr Never Persistent

ZNF264 19 78.3 64.4

ALOX12 7 34.4 21.5

Morales et al, AJRCCM 2012 (185): 937

ALOX12 7 34.4 21.5

EPO 17 15.4 30.8

PDGFB 22 16.5 38


Persistent Difference P value

-13.7 1.4 x 10-5

-12.9 0.003


-12.9 0.003

15.3 0.006

21.4 0.007

Methylation and disease?

- ALOX12 : arachidonate 12 lipoxygenase- Involved in airway inflammation

- Array results confirmed with pyrosequencing, - Array results confirmed with pyrosequencing, although lower methylation levels were observed

- In Menorca Sabadell : 4 CpG Islands in p values 0.019 – 0.168


Methylation and disease?

arachidonate 12 lipoxygenaseInvolved in airway inflammation

Array results confirmed with pyrosequencing, Array results confirmed with pyrosequencing, although lower methylation levels were observed

In Menorca Sabadell : 4 CpG Islands in ALOX12,


SNP affects Methylation

- Association SNP and methylation status in


SNP affects Methylation

Association SNP and methylation status in ALOX12


SNP x M Interaction in asthma? - Interaction of SNP and methylation status in

IL4RA on asthma in the Isle of Wight study

SNP x M Interaction in asthma? Interaction of SNP and methylation status in

on asthma in the Isle of Wight studyRs3024685

CC vs TT

Soto-Ramirez et al, Clin Epigenetics 2013 (5): 1

CT vs TT

Integration: SNPs and methylation

- Model 1: Genetic effect is methylation mediated- SNP � Methylation � Disease

- Model 2: Reverse Causality- Model 2: Reverse Causality- SNP � Disease, Disease

- Model 3: Independent (Common causes)- SNP � Methylation- SNP � Disease

Integration: SNPs and methylation

: Genetic effect is methylation mediatedDisease

: Reverse Causality: Reverse CausalityDisease, Disease � Methylation

: Independent (Common causes)

Liu et al, Nat Biotech 2013 (31): 142-7

Putting it together: integrative genomics

Genome

Transcriptome

Proteome

Putting it together: integrative genomics

Genome

Epigenome

Proteome

B. Raby, personal communication

Genome Wide Association in asthma

• SNPs on chromosome 17q12to asthma in children

Moffatt et al Nature 2007 26;448(7152):470

Genome Wide Association in asthma

SNPs on chromosome 17q12-21 contribute

Moffatt et al Nature 2007 26;448(7152):470-3

17q12-21 SNPs regulate with mRNA expression 21 SNPs regulate with mRNA expression

Verlaan et al, AJHG 2009

a 17q21 DNA variant regulates chromatin remodelling by binding CTCF

CTCF is a protein involved in chromatin looping andis known to reposition nucleosomes, and thus is able to regulate multiple transcripts

a 17q21 DNA variant regulates chromatin remodelling by binding CTCF

Verlaan et al, AJHG 2009

CTCF is a protein involved in chromatin looping andis known to reposition nucleosomes, and thus is able to regulate multiple transcripts

Dna, methylation, environment, disease? Dna, methylation, environment, disease?

So….

MethylationMethylation

So….

AsthmaAsthma

So….

Environment

Methylation

So….

Methylation Asthma

So….

Environment

Methylation

Genetics

So….

Methylation Asthma

This presentation





This presentation




EWAS in asthma: the first results

- MEDALL Project: collaboration in Europe- BAMSE, Sweden- PIAMA, the Netherlands- EDEN, France- EDEN, France- INMA, Spain

- Paired samples of cord blood or blood DNA0 and 4/5 years: EDEN, INMA4/5 and 8 years: BAMSE, PIAMA

- Illumina 450 k Array, including 2 controls

EWAS in asthma: the first results

MEDALL Project: collaboration in Europe

PIAMA, the Netherlands

Paired samples of cord blood or blood DNA0 and 4/5 years: EDEN, INMA4/5 and 8 years: BAMSE, PIAMA

Illumina 450 k Array, including 2 controls

Xu et al, in preparation, 2014

450K Methylation array

• Successor of 27K methylation array

• Similar to Infinium II technique, but some technique, but some differences:– Bisulphite conversion– 2 types of chemistries

on 1 beadchip• Sensitive to batch

effects

450K Methylation array

Future of epigenetics in asthma and allergy? Future of epigenetics in asthma and allergy?

Epigenetics in asthma and allergy

• Epigenetics regulates gene expression

• There are not 4 but 6 basepairs

• Epigenetic mechanisms may explain important observations in asthma

• Environment may change epigenetic signatures: smoking, air pollution


Epigenetics regulates gene expression

There are not 4 but 6 basepairs

Epigenetic mechanisms may explain important observations in asthma

Environment may change epigenetic signatures: smoking, air pollution


• Tissue specific studies are important, further analysis of mixed cell types (blood) is needed

• First EWAS in asthma is underway• First EWAS in asthma is underway

• Next step: Functionally important? How relevant is 5 % difference in gene methylation


Tissue specific studies are important, further analysis of mixed cell types (blood)

First EWAS in asthma is underwayFirst EWAS in asthma is underway

Next step: Functionally important? How relevant is 5 % difference in gene

Epigenetics in asthma

• Need for integration: systems approach to genomics–To understand cause and effect–To understand disease mechanisms–To understand disease mechanisms

• The good news: –Epigenetic modifications can be changed.

New therapeutic options?


Need for integration: systems approach to

To understand cause and effectTo understand disease mechanismsTo understand disease mechanisms

Epigenetic modifications can be changed. New therapeutic options?

Thank you !

MedALL Collaborators

BAMSEErik Melen, Magnus Wickman

EDENIsabelle Annesi -MaesanoIsabelle Annesi -Maesano

INMAJordy Sunyer

PIAMAJet Smit, Alet Wijga, Bert Brunekreef, Johan de Jongste

MEDALL CoordinatorsJean Bousquet and JosepAnto

Thank you !


Cheng XuDirkje PostmaMarjan KerkhofCisca WijmengaCisca WijmengaSoesma MedemaPieter van der VliesColleagues, Pediatric

Pulmonology and Pediatric Allergology

Benjamin Raby, Harvard Medical School, Boston MA

www.bronchitis9.nlwww.bronchitis9.nl

Documents

Epigenetics Asthma Denmark Koppelman 2014 ... · • Role of DNA methylation in astma. T cell differentiation Gene Mechanism IL4 Demethylation of GATA4 binding site Demethylation