“Epigenetica en Biomedicina - Món UVic · “Epigenetica en Biomedicina: Del Conocimiento al Desarrollo Biotecnológico y Farmacéutico” Dr. Manel Esteller [email protected]

“Epigenetica en Biomedicina:

Del Conocimiento al Desarrollo

Biotecnológico y Farmacéutico”

Dr. Manel Esteller

[email protected]

Director

Cancer Epigenetics and Biology Program (PEBC),

Bellvitge Biomedical Research Institute (IDIBELL)

ICREA Research Professor

Professor of Genetics, University of Barcelona

WE ARE MORE THAN OUR GENES !

DOLLY

inrecentyearsepigeneticalterationshavecometopr

ominenceincancerresearchinparticularhypermethy

lationofcpgislandslocatedinthepromoterregionso

ftumorsuppressorgenesisnowfirmlyestablishedasa

nimportantmechanismforgeneinactivationincancer

oneofthemostremarkableachievementsinthefieldha

sbeentheidentificationofthemethylcpgbindingdom

ainfamilyofproteinswhichprovidemechanisticlink

sbetweenspecificpatternsofdnamethylationandhis

tonemodificationsalthoughmanyofthecurrentdatai

ndicatethatmethylcpgbindingproteinsplayakeyrol

einmaintainingatranscriptionallyinactivestateo

fmethylatedgenesmbd4isalsoknowntobeinvolvedine

xcisionrepairoftgmismatchesthelatterisamembero

fthisfamilyofproteinsandappearstoplayaroleinre

ducingmutationsat5methylcytosinethisreviewexam

inesthecontributionofmethylcpgbindingproteinsi

ntheepigeneticpathwayofcancer

The Epigenetic Dice:

-DNA Methylation

-Histone Modifications

-ncRNAs

-….

Cover by Sanchez-Mut and Esteller, Dev Cell, November 15th 2010

Epigenetics Parameters

Nature, 429, 457-63, 2004

Imprint of famine seen in genes of Second World War babies 60 years on

Towards the Human Epigenome

50-year-old

A

C

B

D

3-year-old twins 50-year-old twins3-year-old twins 50-year-old twins

0,00

0,40

0,80

1,20

1,60

2,00

0 15 30 45 60 75

Age (years)

ES

D 5

mC

0,00

0,40

0,80

1,20

1,60

2,00

0 15 30 45 60 75

Age (years)

ES

D A

c H

4

0,00

0,40

0,80

1,20

1,60

2,00

0 15 30 45 60 75

Age (years)

ES

D A

c H

3Francis Collins, director of the National Human Genome Research Institute, said:

"Here's something where Mendel, Watson and Crick all seem to have missed some crucial goodies"

Heyn et al., Carcinogenesis 2012

Discordant Twins for Breast Cancer

Autoantibodies against nuclear antigens, specially against DNA, histones and

nucleosomes

Lupus eritematoso sistémico

Autoimmune disease affecting many tissues and organs

% m

eth

yla

tion T

win

A

20-yo

twins

0 0.20 0.40 0.60 0.80 1

082_02 AVG_Beta

082_01 AVG_Beta vs 082_02 AVG_Beta

0

0.20

0.40

0.60

0.80

1

082_01 A

VG

_B

eta

Average Healthy Twin

Ave

rag

e S

LE

Tw

in

TD2 - twins (397 - 398)

0 0.20 0.40 0.60 0.80 1

030_02 AVG_Beta


0

0.20

0.40

0.60

0.80

1

030_01 A

VG

_B

eta


Ave

rag

e S

LE

Tw

in

% methylation Twin B

% m

eth

yla

tion

Tw

in A

TD2 - twins (529 - 530)

0 0.20 0.40 0.60 0.80 1

061_02 AVG_Beta


0

0.20

0.40

0.60

0.80

1

061_01 A

VG

_B

eta


Ave

rag

e S

LE

Tw

in

Epigenetics, Discordant Twins and Disease

Diabetes Type 2, Target tissue: Fat

Systemic Lupus Erythematosus, Target tissue: Lymphocytes

A

C

AF CA AS

0 2

0 4

0 6

0 8

0 1

00

An

cestr

al a

llele

(%

) P

CA

1

PCA2

-2 -1

0 1 2

-2 -1 0 1 2

D

B

AF AS CA

40 60 8

0 1

00 1

20

100 100

99

100

au

He

igh

t

Han Chinese-American (AS)

Caucasian-American (CA)

African-American (AF)

DNA methylation contributes to natural human variation

Heyn et al., Genome Research 2013

DNA methylation and natural human variation: pathways and diseases


Taste Skin Pigmentation

http://www.google.es/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&docid=j0_4Rq-xSbiQAM&tbnid=pLNLqB3T0LIjeM:&ved=0CAUQjRw&url=http://www.dermacaredirect.co.uk/blog/welcome-to-our-september-2012-newsletter/&ei=MtRXU9T9BKHW0QXIkoGYCg&psig=AFQjCNE1h7aMzGmMGqf-XG0Qie9al1f5TA&ust=1398351259693040


Diabetes

Parkinson’s

Infection

(HBV, HIV, Measles

Virus, E. coli)

Taste Skin Pigmentation

http://www.google.es/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&docid=j0_4Rq-xSbiQAM&tbnid=pLNLqB3T0LIjeM:&ved=0CAUQjRw&url=http://www.dermacaredirect.co.uk/blog/welcome-to-our-september-2012-newsletter/&ei=MtRXU9T9BKHW0QXIkoGYCg&psig=AFQjCNE1h7aMzGmMGqf-XG0Qie9al1f5TA&ust=1398351259693040

DNA methylation plasticity of human adipose-derived stem cells in lineage commitment

- 293 + 92PTPRS

Re

gre

sse

d

Ste

mC

ells

(fro

mm

yo

cyte

s)

- 152 + 160PIWIL2

Re

gre

sse

d

Ste

mC

ells

(fro

mo

ste

ocyte

s)

Re

gre

sse

d

Ste

mC

ells

(fro

mm

yo

cyte

s)

- 159 + 162SAA1

Re

gre

sse

d

Ste

mC

ells

(fro

mo

ste

ocyte

s)

Re

lative

exp

ressio

n

(PT

PR

S v

s G

AP

DH

)

0

200

400

600

800

1 2 3

Re

lative

exp

ressio

n

(SA

A1

vs G

AP

DH

)

0

50

100

150

1 2 3

Re

lative

exp

ressio

n

(PIW

IL2

vs G

AP

DH

)

0

50

100

150

1 2 3 4 5

A

B C

OSTEOGENIC

Differentiation

medium

Suppression of

the inductorDifferentiation

medium

Suppression of

the inductor

MYOGENIC

- 293 + 92PTPRS

Adult

Stem Cells_1

Adult

Stem Cells_2

In vitro

myocytes_1

In vitro

myocytes_2

- 152 + 160PIWIL2

Adult

Stem Cells_1

Adult

Stem Cells_2

In vitro

myocytes_1

In vitro

osteocytes_2

Adult

Stem Cells_1

Adult

Stem Cells_2

In vitro

Osteocytes_1

In vitro

Osteocytes_2

- 159 + 162SAA1

Berdasco et al., American Journal of Pathology 2012

Differentiation upon siRNA of SIRT1

Differentiation upon bFGF withdrawal

Embryonic Stem Cells (H-181)

Blue: DAPI

Green: alpha-actin

(mesodem)

Differentiation upon Sirtinol treatment (24h)

Stem Cells and Sirtuins

Epigenetic Marks

The Epigenetic Marks: DNA Methylation

Esteller, Nat Rev Genet 2007

Esteller, New England Journal of Medicine, 2008

Heyn and Esteller, Nature Review Genetics, 2012

Roriguez-Paredes and Esteller, Nature Medicine, 2011

THE HISTONE CODE

H3, N-terminus H4, N-terminus

SGRGKGGKGLGKGGAKRHRKVLRDN- 8 12 16 20 5

Ac

Ac Ac Ac Ac Me

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPH- 4 9 18 10 14 23 27 36

Me

Ac Me P Ac

activa

tio

n

sile

ncin

g

The Dark Genome

Melo and Esteller, FEBS Letters, 2010

Melo and Esteller, FEBS Letters, 2010

Nature Genetics, 2009

Science, 2009

Cancer Cell, 2010

Esteller, Nature Reviews Genetics 2011

Rodriguez-Paredes and Esteller, Nature Medicine, 2011

Epigenetic drugs

DNA Demethylating Agents

Histone Deacetylase Inhibitors

microRNA Related Compounds

Histone Methyltransferase Inhibitors

Histone Demethylase Inhibitors

Histone Kinase Inhibitors

Histone Acetyltransferase Inhibitors

Bromodomain Inhibitors

Sirtuin Inhibitors

Preclinical

stage

Clinical

stage

Rodriguez-Paredes and Esteller, Cancer Discovery 2011

Outside Cancer

Rett Syndrome (RS) is a neurodevelopmental disorder believed to affect 1 in

10,000 females..

Germline mutations in MECP2 (Methyl-CpG Binding Protein-2) found in

65% of Rett patients. MECP2 is located in Xq28.

Girls with Rett Syndrome appear to develop normally until 6 to 18 months of

age. They then enter a period of regression, losing speech and hand skills

they had acquired. Most girls develop seizures, repetitive hand movements,

irregular breathing and motor-control problems. A slowing of the rate of

head growth also becomes apparent. Most researchers agree that RS is a

developmental disorder rather than a progressive, degenerative disorder.

The girls can live to adulthood, but most never regain the ability to use their

hands or to speak.

Rett Syndrome

No

Mu

t3

No

Mu

t1

No

Mu

t4

No

Mu

t2

R255X

T158M

R106W

R306C

R294X

P391X

125 123 126 112 125 120 56 53 77 7136 38 35 49 36 41 105 108 84 90

No

Mu

t3

No

Mu

t1

No

Mu

t4

No

Mu

t2

R255X

T158M

R106W

R306C

R294X

P391X

125 123 126 112 125 120 56 53 77 7136 38 35 49 36 41 105 108 84 90

Clustering expression analysis and

release of MeCP2- Silencing

in Rett Syndrome Patients

MPP1

Control

R106W

I UB B UB B

MeCP2 NAB

+ 103

N1

N2

- 264

N2

Gene Primer sequence Annealing

MPP1 Forward 5´-YGAATTTGGTTAGGGTATTYGGG-3´ 57 ºCReverse 5´-CTTAAAAATCATCTCRCAAAAACT-3´

MPP1

Human Mutation, 2005

http://www.rett.es/gif/revista/editorial2.html

1.-Encéfalo 2.-Mesencéfalo 3.-Cerebelo

1

2 3

1

2 3

310mg

299mg 7.5gr/10.25cms

8.1gr/11.05cms

Mouse Model of Rett

Dynamic DNA Methylation Reconfiguration During Brain Development

Lister et al., Science 2013

•DNA Methylation and Schizophrenia

DNA Methylation Map of Mouse Brain Identifies Targets of Epigenetic Disruption in Alzheimer’s Disease

Sanchez-Mut et al., Brain 2013

Promoter hypermethylation of the phosphatase DUSP22 mediates PKA-dependent

TAU phosphorylation and CREB activation in Alzheimer's disease

Sanchez-Mut et al., Hippocampus 2013

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=cAxSNZXvQ-L1NM&tbnid=vD3j8-Ie1YppWM:&ved=0CAUQjRw&url=http://commons.wikimedia.org/wiki/File:DNA_microarray.svg&ei=4yndUof5Bqqm0wWK_oCYAg&bvm=bv.59568121,d.d2k&psig=AFQjCNGJkTh-CebD4Ips9_ftEtpMB3yALA&ust=1390312271074176

DNA Methylation Profiling of Human Atheroesclerosis

Zaina et al., Circulation: Cardiovascular Genetics 2014

…Epigenomes

“The Book of Life” (Almost…)

Epigenetic differences

in monozygotic twins

and distinct penetrance

of disease


in cloned animals

and distinct phenotypes


among species

and distinct skills


among species

and distinct skills

Epigenetic

alterations

and human

diseases

Epigenetic

changes

in germinal

cells

Epigenetic

changes in

development

and growth

Figure 1 Esteller

Esteller, The Lancet, 2008

Heyn and Esteller, Nature Reviews Genetics, 2012

Group 1 A.

Group 2

0 0.5 1

Adeno

Squamous

Large

0 20 5 10 15

0

0.2

0.4

0.6

0.8

group2 (n=174)

group1 (n=24)

1.0

Pro

po

rtio

n w

ith

rec

urr

ence

-fre

e su

rvia

l

Years after surgery

p: 0.002

Hazard ratio, 2.30 (95% CI, 1.36-3.89)

B.

Group 1 C. Group 2

0 0.5 1

group2 (n=114)

group1 (n=33)

p: 0.005

Hazard ratio, 2.46 (95% CI, 1.32-4.59)

D. Adeno

Squamous

Large

0 20 5 10 15

0

0.2

0.4

0.6

0.8

1.0

Pro

po

rtio

n w

ith

rec

urr

ence

-fre

e su

rvia

l

Years after surgery

A 450,000 CpG Site Prognostic Classifier of 500 Non-Small Cell Lung Cancer Patients

Cancer of Unknown Primary

Distance correlation to closest CpG site

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

0.80

0.90

1.00

Promoter Exonic Intronic Intergenic

Mean

meth

yla

tio

n level

NB

Y103

**

** ** **

68%

70%

72%

74%

76%

78%

80%

82%

Cp

G m

eth

yla

tio

n

lev

el (%

)

NB Y103 Y26 Corr

ela

tio

n

Distance

0.1

1.0

10 100 1 1000

16,000,000

16,200,000

16,400,000

16,600,000

16,800,000

Me

thyla

ted

Cp

G s

ite

s

NB Y103 Y26

Chromosome 8

0.8

0.6

0.4

Meth

. le

vel

Chromosome 2

0.8

0.6

0.4

Meth

. le

vel

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

CG poor promoters

CGI promoters

Me

an

me

thyla

tio

n le

ve

l

NB

Y103

**

**

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

Promoter Exonic Intronic Intergenic

DM

R n

um

be

r

CpG poor

promoters CpG island

promoters

671; 83%

140; 17%

585; 55%

479; 45%

15669;

87%

2261; 13%

Hypomethylated

in Y103Hypermethylated

in Y103

DMRs

Housekeeping genes Tissue-specific genes

56; 87%

8; 13%

1200; 66%

611; 34%

The Distinct DNA Methylomes of Newborns and Centenarians

Proc Natl Acad Sci USA, 2012

Nonagenarians Newborn HG/W

Diseases Associated with Premature Aging:

Hutchinson-Gilford Progeria and Werner syndrome

Prediction of Biological Age Using DNA Methylation

The Genome

The Biomedical Iceberg

The Epigenome

Manel Esteller, 2014

[email protected]

Documents

“Epigenetica en Biomedicina - Món UVic · “Epigenetica en Biomedicina: Del Conocimiento al Desarrollo Biotecnológico y Farmacéutico” Dr. Manel Esteller [email protected]