“Epigenetica en Biomedicina: Del Conocimiento al Desarrollo Biotecnológico y Farmacéutico”

Dr. Manel Esteller [email protected]

Director and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL)

ICREA Research Professor Professor of , University of

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

A B 2,00 2,00 2,00

1,60 1,60 1,60

1,20 1,20 1,20

0,80 0,80 0,80

ESD 5mC

ESD Ac H4 ESD Ac H3

0,40 0,40 0,40

0,00 0,00 0,00 0 15 30 45 60 75 0 15 30 45 60 75 0 15 30 45 60 75 Age (years) Age (years) Age (years) C D

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

Francis 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" Discordant Twins for Breast Cancer

Heyn et al., Carcinogenesis 2012 Lupus eritematoso sistémico

Autoimmune disease affecting many tissues and organs

Autoantibodies against nuclear antigens, specially against DNA, histones and nucleosomes % methylation Twin A Average0 8 2 _ 0 1 A SLEVG _ B eTwinta 0.20 0.40 0.60 0.80 Diabetes Diabetes Type 2, Targettissue: Fat Systemic Systemic LupusErythematosus, Target tissue:Lymphocytes 0 1 0 Epigenetics, Epigenetics, Discordant Twinsand Disease 0.20 082_01 AVG_Beta vs AVG_Beta 082_02 AVG_Beta 082_01 Average Average Healthy Twin 082_02 AVG_Beta 0.40 0.60

0.80 twins 20 1 - yo

Average SLE Twin 0 3 0 _ 0 1 A V G _ B e ta 0.20 0.40 0.60 0.80 0 1 0

Average Average Healthy Twin 0.20 030_01 AVG_Beta vs AVG_Beta 030_02 AVG_Beta 030_01 030_02 AVG_Beta 0.40 0.60 TD2 -

twins (397

0.80 - 1 398)

Average0 6 1 _ 0 SLE1 AVG _TwinB e ta 0.20 0.40 0.60 0.80 % methylation Twin A 0 1

0

0.20 061_01 AVG_Beta vs AVG_Beta 061_02 AVG_Beta 061_01 % Average Healthy Twin methylation

061_02 AVG_Beta 0.40 Twin B 0.60

TD2

0.80 - twins (529

1 - 530)

DNA methylation contributes to natural human variation

au

100 A African-American (AF) B 100 100 Caucasian-American (CA) 99

Han Chinese-American (AS)

Height 40 60 80 100 120 100 80 60 40

C AF AS CA

PCA1

1 0 1 2 1 1 0

-

2 2 - -2 -1 0 1 2 PCA2 AF CA AS

D

Ancestral allele allele (%) Ancestral 0 20 40 60 80 100 80 60 40 20 0 Heyn et al., Genome Research 2013

DNA methylation and natural human variation: pathways and diseases DNA methylation and natural human variation: pathways and diseases

Taste Skin Pigmentation DNA methylation and natural human variation: pathways and diseases

Taste Skin Pigmentation

Diabetes Infection (HBV, HIV, Measles Parkinson’s Virus, E. coli)

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

A OSTEOGENIC MYOGENIC PTPRS - 293 + 92 Differentiation Suppression of Differentiation Suppression of medium the inductor medium the inductor

Adult Stem Cells_1

Adult Stem Cells_2

In vitro myocytes_1 PTPRS B - 293 + 92 C In vitro 800 myocytes_2

600 )

expression 400 SAA1

- 159 + 162 Cells 200

myocytes

PTPRS vs GAPDH) vsPTPRS

Relative

(

tem S Regressed 0

1 2 3

from ( Adult Stem Cells_1 SAA1 Adult - 159 + 162 Stem Cells_2

) 150

In vitro Osteocytes_1

Cells 100

expression osteocytes

In vitro tem S

Osteocytes_2 Regressed 50

from

(

SAA1 vs GAPDH)vsSAA1

( Relative 0 1 2 3 PIWIL2 PIWIL2 - 152 + 160

- 152 + 160 )

Adult 150

Stem Cells_1 Cells

100 osteocytes

Adult tem S

Stem Cells_2 Regressed expression

from 50

(

)

PIWIL2 vs GAPDH) vs PIWIL2 Relative

In vitro ( myocytes_1 0

1 2 3 4 5 Cells

In vitro myocytes

osteocytes_2

tem

S

Regressed

from (

Berdasco et al., American Journal of Pathology 2012 Stem Cells and Sirtuins Blue: DAPI Green: alpha-actin Embryonic Stem Cells (H-181) Differentiation upon siRNA of SIRT1 (mesodem)

Differentiation upon Sirtinol treatment (24h) Differentiation upon bFGF withdrawal

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

Me Ac P Ac Me Ac Ac Ac Ac

activation 4 9 10 14 18 23 27 36 5 8 12 16 20

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPH- SGRGKGGKGLGKGGAKRHRKVLRDN-

Me Ac silencing The Dark Genome Melo and Esteller, FEBS Letters, 2010 Melo and Esteller, FEBS Letters, 2010

Nature Genetics, 2009

Cancer Cell, 2010

Science, 2009 Esteller, Nature Reviews Genetics 2011 Rodriguez-Paredes and Esteller, Nature Medicine, 2011 Preclinical Clinical Epigenetic drugs stage stage DNA Demethylating Agents

Histone Deacetylase Inhibitors

Histone Methyltransferase Inhibitors

Histone Demethylase Inhibitors

Histone Kinase Inhibitors

Histone Acetyltransferase Inhibitors

Bromodomain Inhibitors

Sirtuin Inhibitors

microRNA Related Compounds

Rodriguez-Paredes and Esteller, Cancer Discovery 2011 Outside Cancer Rett Syndrome

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.

+ 103 +

N2

B MPP1 57 ºC 57

Annealing Silencing Silencing NAB

UB -

Human Human Mutation, 2005 B

MeCP2 UB

I

5´-CTTAAAAATCATCTCRCAAAAACT-3´ 5´-YGAATTTGGTTAGGGTATTYGGG-3´ Control R106W MPP1

Primer sequence Forward Reverse 264

- in Rett Syndrome Patients Syndrome Rett in

Gene MPP1 N2 N1 release of MeCP2 of release

Clustering expression analysis and and analysis expression Clustering NoMut3

NoMut1

NoMut4

NoMut2

R255X

R306C

R294X

P391X

T158M

R106W 36 36 38 38 35 35 49 49 36 36 41 41 105 105 108 108 84 84 9090 125 125 125 123 123 126 126 112 112 125 125 120 120 56 56 53 53 77 77 7171

Mouse Model of Rett

1

3 2

7.5gr/10.25cms 1.-Encéfalo 299mg 2.-Mesencéfalo 3.-Cerebelo

1 3 2

8.1gr/11.05cms 310mg 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 DNA Methylation Profiling of Human Atheroesclerosis

Zaina et al., Circulation: Cardiovascular Genetics 2014 …Epigenomes “The Book of Life” (Almost…) Figure 1 Esteller Epigenetic differences in monozygotic twins and distinct penetrance of disease

Epigenetic differences among species and distinct skills

Epigenetic differences among species and distinct skills

Epigenetic differences in cloned animals and distinct phenotypes

Epigenetic Epigenetic changes in changes development in germinal and growth cells

Epigenetic alterations and human diseases

Esteller, The Lancet, 2008

Heyn and Esteller, Nature Reviews Genetics, 2012 Heyn and Esteller, Nature Reviews Genetics, 2012 A 450,000 CpG Site Prognostic Classifier of 500 Non-Small Cell Lung Cancer Patients A. B. Group 1 Group 2

Adeno Squamous Large 0 0.5 1 1.0 Hazard ratio, 2.30 (95% CI, 1.36-3.89) p: 0.002

0.8

free free survial - 0.6

group2 (n=174) 0.4

0.2 group1 (n=24)

0 Proportion with recurrence with Proportion 0 5 10 15 20 Years after surgery

C. Group 1 Group 2 D. Adeno Squamous Large 0 0.5 1 1.0 Hazard ratio, 2.46 (95% CI, 1.32-4.59) p: 0.005

0.8

free free survial - 0.6 group2 (n=114)

0.4

0.2 group1 (n=33)

0 Proportion with recurrence with Proportion 0 5 10 15 20 Years after surgery Cancer of Unknown Primary

The Distinct DNA Methylomes of Newborns and Centenarians

16,800,000 82% 1.0 Distance correlation to closest CpG site 80% 16,600,000 78%

76% 16,400,000

74% level (%) level 16,200,000 72%

CpG methylation CpG methylation 70% Methylated Methylated CpG sites 16,000,000 68% NB Y26 Y103 NB Y26 Y103 Correlation

0.8

0.1

1 10 100 1000 0.6 Distance

Chromosome 2 1.00 0.9 ** Meth. level Meth. ** 0.90 ** ** 0.8 0.4 0.80 0.7 0.70 0.6 0.8 0.60 **

0.5 0.50 NB NB 0.40 0.4 Y103 ** Y103 0.30 0.3

0.6 0.20 0.2 Mean methylation level methylation Mean 0.10 level methylation Mean 0.1

Chromosome 8 0.00 0 Meth. level Meth. 0.4 Promoter Exonic Intronic Intergenic CG poor CGI promoters promoters

CpG poor CpG island promoters promoters 140; 17% 479; 45%

9000 8000 DMRs

7000 15669; Hypomethylated 6000 87% in Y103 671; 83% 585; 55% Hypermethylated 5000 in Y103 4000 Tissue-specific genes Housekeeping genes 3000 8; 13% DMR numberDMR 2000 611; 34% 1000 0 2261; 13% Promoter Exonic Intronic Intergenic

1200; 66%

56; 87%

Proc Natl Acad Sci USA, 2012 Diseases Associated with Premature Aging: Hutchinson-Gilford Progeria and Werner syndrome

HG/W Nonagenarians Newborn Prediction of Biological Age Using DNA Methylation The Biomedical Iceberg

The Genome

The Epigenome

[email protected]

Manel Esteller, 2014