Genetics of obesityGenetics of obesityFrom genetics to functional genomics From genetics to functional genomics

Prof. Karine ClémentInserm U872 Nutriomique

Université Paris 6/Cordelier Research CentreEndocrinology and Nutrition Dept, Pitié-

SalpêtrièreParis

Karine.clement@psl.aphp.fr

Genetics of obesityGenetics of obesityfrom genetics to functional genomics from genetics to functional genomics

Contents of presentationContents of presentationSlidesSlides

IntroductionIntroduction 3 – 53 – 5Monogenic obesity: case study BBSMonogenic obesity: case study BBS 6 – 216 – 21Other mono- and oligogenic examplesOther mono- and oligogenic examples 22 – 4122 – 41Polygenic obesity: pertinent genes and risk factors Polygenic obesity: pertinent genes and risk factors 42 – 5742 – 57Gene-gene and gene-environment interactions Gene-gene and gene-environment interactions 58 – 6358 – 63The futureThe future 64 – 6964 – 69Abbreviations usedAbbreviations used 70 - 7170 - 71

Obesity: chronic disease with different stages of development

weig

ht

Intervention

years

Systemic and signal Pathology

Constitution Chronic diseaseAggravation Resistance/Regain

Complications

Genes_ Environment Interaction

Epigenetic events

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Obesity: complex physiopathology

Afferent Signals

GhrelinPYY

InsulinAmylin

IL6Leptin

Adiponectinothers

Hypothalamus

Efferent signals

SympathicParasympathic

Thyroid Hormones

•Hypothesis driven (candidate gene) •Hypothesis generating approach

Genetics of human obesityDissection and strategy

EnvironmentGenes

MonogenicHigh penetrance

Monogenic Low penetranceVariable expression

Polygenic

•Rare cases•Syndromes

•Population study•Genetic epidemiology

•Tissue investigation in clinical trials • “omic studies”Example: Adipose tissue analysis

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Monogenic forms of obesityMonogenic forms of obesity

or obesity cases with strong genetic influenceor obesity cases with strong genetic influence

Strategic « choices »

Human Syndromes

Gene identification

Genome wide scan

Molecular/cellular studiesPhysiology

Clinical cases

Screening of a known gene

Gene mutation

Hypothesis generating Hypothesis raised

Novel disease/Novel syndrome

Hypothesis

BiochemistryGeneticsComparative genomics

From clinical syndromes to genes

Syndrome Name (reference)

Clinical heterogeneity

Trans-mission

Loci / Genes

Prader-Willi Muscular HypotonyMental retardation HyperphagiaHypogonadismShort stature

Autosomic dominantimprinting

15q11SRNPNMicro deletion Maternal Disomy

Bardet-BiedelMykytyn Nature Genet 2002

HypogonadismPigmentary retinopathyPolydactylyMental retardation

Autosomic recessive

BBS (1-12)chaperonin Protein MKKS (Chr 20)Ciliary cells proteins

AlströmHearn Nature Genet 2002Collin Nature Genet 2002

MyocardiopathySensory deficit (retinopathy, deafness)Dyslipidemia, diabetes

Autosomique recessive

2p14ALMS1

Börjson-Forssman-LehmanLower Nature genet 2002

Morbid obesity, epilepsyHypogonadism, facial dysmorphy

Xq26.3 / Plant homeodomain like finger gene

Bardet-Biedel Syndrome (BBS)

PolydactylyObesity inchildhood (75%)

Retinitis pigmentosa

…. And other diseases (uro-genotal anomalies, kidney malformation) and cognitive dysfunction

Discovered in the late 19th centuriesKnown as a monogenic disease

BBS: ideal case for gene discovery

• Frequency of the disease was known– (1 in 150,000 in Europe, higher in Asia/North

Africa)• Monogenic (1 gene, 1 disease well identified)• Mode of transmission known (recessive)• Phenotype easy to detect• Case, Family, samples accessible

Statistics models and tools appropriate

1 to 2 years (<6 months)

400-800 Markers400-800 Markers400-800 Markers400-800 Markers Fine MappingFine MappingFine MappingFine Mapping Many GenesMany GenesMany GenesMany Genes Extensive Extensive SNP AnalysisSNP Analysis

Extensive Extensive SNP AnalysisSNP Analysis

Therapeutic Target

Family Collection

Loci 15-30 Mb Loci 15-30 Mb Loci ~ 5 Mb Loci ~ 5 Mb

Microsatellite genotypingMicrosatellite genotyping > 500 subjects Parents & Children

Current Genome scanning approach

Infrastructure:Automated Sequencers

PCR machinesLiquid handling robotsRunning costs: High

Infrastructure:Automated SNP system

PCR machinesLiquid handling robotsThousands of samples

Running cost: High

Family collections

Linkage analysis

LOD-score analysis

(homozygosity mapping)

Sib-pair analysis TDT

Tests the co-segregation of

alleles in (large)non-linkage

Tests the distribution alleles IBD among affected sib

pairs against H0=1/2

Tests the transmission of alleles from hetero-zygous

parents to offspring against H0=1/2

Linkage analysis in complex disease

Qualitative traitsMethod of sibling pairs

(principals)

Father AB and Mother CD If the first child is AC

The second child could be AC AD BC BD

Number of identical alleles (IBD) 2 1 0

Proportion of identical alleles (xi) 1 1/2 0

Probability (pi) 1/4 1/2 1/4

Proportion of alleles IBD = PIXI =

Absence of linkage: = ½. If ≥ 1/2 test for linkage (t)

CDAB

AC ?

Quantitative trait linkage analysis

Fine mapping strategy in family collectionsFine mapping strategy in family collections

• Positional candidate SNP mapping

• Obese controls studies• Sib-TDT analysis

1

2

3

M1 M1 M1 M1 M11 cM

Collection 1Collection 1

Linkage with markersLinkage with markers Linkage confirmedLinkage confirmed

Collection 2Collection 2•Increased samplesIncreased samples•Increased markers at locusIncreased markers at locus•SNP maps, combine haplotypesSNP maps, combine haplotypes

BBS: 1st surprising result

Multiple genes involved in BBS

*

*

*

* Genome wide scan + comparative genomics

BBS genes encode unknown proteins or ones related to primary cilium. It is a model of ciliopathy

Nom Locus Gene ProteinBBS1 11q13 BBS1 Ciliary protein

(M390R mutation 80%)BBS2 16q21 BBS2 Ciliary ProteinBBS3 3p13 BBS3 G-ADP ribosylationBBS4 15q22 BBS4 PCM1 recruitment

(pericentriolar material protein)BBS5 2q13 BBS5 synthesis cilia flagellaBBS6 20p12 MKKS McKusick-Kaufman

(chaperonin)BBS7 4q27 BBS7 Ciliary protein

(close to BBS 1 & 2)BBS8 14q32 BBS8(TTC8) Cell Motility (primary cilia)BBS9 7p14 PTHB1 regulated by ParahormoneBBS10 12q BBS10 Chaperonin Protein (new)*BBS11 9q33.1 BBS11 ? UnconfirmedBBS12 4q27 BBS12 Chaperonin Protein (new)*

BBS: 2nd surprising result

Copyright ©2005 American Physiological Society

Davenport, J. R. et al. Am J Physiol Renal Physiol 289: F1159-F1169 2005;doi:10.1152/ajprenal.00118.2005

Motile or immotile (primary) cilia are located on the surface of nearly every cell within the mammalian body

Copyright ©2005 American Physiological Society

Davenport, J. R. et al. Am J Physiol Renal Physiol 289: F1159-F1169 2005;doi:10.1152/ajprenal.00118.2005

Primary cilia function in tubules as sensors for fluid flow

Dysfunction of movement regulation(BBS7,8)

BBS: 3rd surprising result

In some BBS families there is a triallelic mode of transmission (genetic epistasis)

BBS1

Homozygous

BBS4 Heterozygous

Phenotype

Adapted from Mutch & Clement, Plos genet 2006

BBS: from syndrome to genesand novel pathophysiological mechanisms

- Oligogenic and not monogenic (12 genes at least; more to be discovered) - recessive autosomic but also triallelic transmission (12/65 families with BBS mutation have another BBS mutation) - More heterogeneous than thought- Opened a new field of research in human pathology : BBS is a ciliopathy

More to be discovered-Role in energy regulation-Gene-phenotype-Role/mechanisms in common obesity

Strategic « choices »

Human Syndromes

Gene identification

Genome wide scan

Molecular/cellular studiesPhysiology

Clinical cases (disease = associated features)

Screening of a known gene

Gene mutation

Hypothesis generating Hypothesis raised

Novel disease/Novel syndrome

Hypothesis

BiochemistryGeneticsComparative genomics

LeptinLeptin Insulin Ghrelin

POMCPC1PC2

α-MSHβ-MSH

Arcuate Nucleus Paraventricular Nucleus

MC4-R

AGRP

NPY AGRP

LepR

LepRIR

GHR

Adipose

tissue

Pancreas Stomach

IR

α-MSH

β-MSH (?)

+

+

-

- +-

HYPOTHALAMUS

SIM1

BDNFTKRB

?

VentromedialNucleus

Energy balance

Human mutations

Monogenic obesity affecting the leptin/melanocortin pathway

Mutch & Clement, 2006

Morbid obesity in two cousins

Seru

m lep

tin c

once

ntr

ati

on (

ng m

l-1)

Ob1 and Ob2heterozygote siblingnormal siblings

heterozygote mothersheterozygote fathers

95% confidence intervalsof the mean

normal childrennormal adults

Inappropriate leptin levels based on corpulenceexamination

Nature, 387, pp 903-908June 26, 1997

7q31

1 2 35’ 3’10kb 1.9kb

cEBP

AAAAcDNA= 3.5 kbGene= 18kb

167 aaLeptin

Leptin* 133aa

*

*

*

Homozygous G del codon 133

Modified by Coll et al., 2004

POMC post-transcriptional processingPOMC post-transcriptional processing

PC1 cleavage site Hypothalamus products

PC2 cleavage site Anterior Pituitary products

NH2 COOH

N-teminal JP ACTH Β-LPH

γ3-MSH

γ1-MSH

α-MSH CLIP

γ-LPH

β-MSH β-end1-27

ssss

MC1-R MC4-RMC2-R

Adrenal gland HypothalamusSkin

Eumelanin pigment Synthesis Feeding inhibitionGlucocorticoids

POMC

POMC and derived actions

ACTH

ACTH

MSHMSH

ssss

MC1-R MC4-RMC2-R

Adrenal HypothalamusSkin

Eumelanin pigment Synthesis Feeding inhibitionGlucorticoids

POMC

MSH

POMC and derived actions•Compound heterozygous for exon 3 mutation (G->T nt7013 & del at 7133)•No ACTH and aMSH synthesis

(Krude et al, Nature genet, 1998)

ACTH MSH

POMC aberrant proteins in humans

Adapted from Krude, JCEM, 2003

• Severe obesity• Post-prandial Hypoglycemia• Hypogonadism• Hypocortisolism • ProInsulin /Insulin & POMC increased• Compound heterozygous for 2 mutations

(Gly483Arg, exon13, A->C intron4 with deletion exon 5)

• Anomaly of maturation of prohormones (Proinsuline, POMC),

• but also of gut hormones– (GLPs), leading to intestinal dysfunction

Mutation of Proconvertase 1 O’Rahilly et al, NEJM, 1995 &Jackson et al, Nature Genet 1997, Jackson, Nat Genet 2003

Fraction Number

Normal Pathways of Processing and effects of the Putative Defect in Prohormone Convertase 1 in the Study Patient

5*Humans 3* 6* 1* ?

Food intake

Energy expenditure

Leptin and melanocortin mutations

Adapted from D Cummings, 2003

Rare syndromes Obesity only

Ob Db POMC-/- fat Mc4r (-/-) Obese phenotypeMice

305

EVFVTLG

VISLLENI

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249

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151

131

120

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70

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80

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97

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145 163

174

168

195

179

211

253

242

260

281

298

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Extracellular

Intracellular

More than 90 mutations in MC4R gene…..2-3% obesity cases

Early weight gain

in children with MC4R mutations

(French children)

MC4R homozygote ( AG 346-347)

MC4R homozygote (I166V)

MC4R heterozygote children (13)

Obese children with wild type MC4R (40)

10,00

12,00

14,00

16,00

18,00

20,00

22,00

24,00

26,00

28,00

30,00

32,00

34,00

36,00

38,00

40,00

42,00

44,00

46,00

48,00

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52,00

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56,00

58,00

60,00

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66,00

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0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18Age (ans)

IMC

P97

P95

P90

P75

P50

P25

P5

Homo (V166I)

LepR 1

LepR 2

Non mutes

Het MC4R

97P

50P

LepR

Mutation

LepR

Mutation

Clement Nature 1998 ; Dubern, et al J Pediatr 2001 and 2007

LEPR mutation

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Membrane expression

Receptor activity

Genotype-phenotype Relationships

Functional consequences of MC4R mutations

AGRP

AC

N

C

AMPc

?

X

MSH

Intracellular retention => 56% of MC4R mutations

Deficit of MSH response80% of MC4R mutation

Decreased basal activity=> 76% of MC4R mutations

Intracellular retention associated with early onset obesity

Lubrano-Berthelier et al, HMG 2003Srinivasan et Lubrano-Berthelier et al JCI 2004Lubrano-Berthelier et al, JCEM 2006

Food Intake

Energy homeostasis

Prot Gs

+-

Data from the French population

Evidence that MC4R is an “obesity gene”

• Biological candidate • Invalidation in mouse

models leads to obesity (KO)

• Population-based association studies

• “Co-segregation” of genotype and phenotype in families

• Loss of function of variant receptors

European populations screened(>5000 obese screened, >8000

controls) UK (Farooqi &Yeo NEJM 03, Hum Mol

Genet 03, JCI 00, Nature Genet 98) Finland (Valli-Jaakola, JCEM 04) France (Lubrano, Dubern, Clément

Vaisse, Diabetes 04, JCEM 04, Hum Mol Genet 03, J Ped 00, JCI 00, Nature genet 98, JCEM 06)

Germany (Hinney & Hebebrand, Am J Hum Genet 04, JCEM 03, Mol Psy02, Am J Hum Gent 99, Biebermann H, JCEM 06)

Italy (Miraglia Del Giudice, JIO 02, Buono 05)

Spain (Marti IJO 03) Switzerland (Branson, NEJM 03) Denmark (Larsen, JCEM 2005)

Invalidation in mouse models leads to obesity (KO)

Population based association studies (no linkage)

Co segregation of genotype and phenotype in families

Loss of function of variant receptors

Review in Govaerts Peptide 2005

MC4R mutations illustrate the issues raised by predictive medicine in obesity

• High risk of developing obesity in carriers notably in infancy• We cannot know when and how

– variable expression, interaction with environment and/or genes, role of Val103Ile as a modulator of the phenotype (Dempfle 2004, Heid 2005)

– Phenotype variation with time

• Or if obesity will develop – incomplete penetrance

• Functional consequences are heterogeneous – effect of MC4R powerful agonists ?

• Physicians have to agree about methods of prevention of obesity in the predisposed families (family counseling ?)

Other oligogenic situations in obesity

ARG236GLY mutation in the POMC gene leads to EARLY-ONSET OBESITY in children

• Good biological candidate• Co-segregates with obesity in families • Frequency increased in obese (0.88) vs controls

(0.22)• Disruption of the dibasic cleavage site between

(beta-MSH) and beta-endorphin reduces its ability to activate MC4R

• Replication is needed

Is POMC the second oligogene ?

Challis Hum Mol Genet 2002

Treatment of leptin-deficient children

Food intake Weight S Farooqi and S O’Rahilly’s group

Leptin treatment in adultshomozygous Cys105Thr (Licino, PNAS, 2004)

C B AY 40 35 27BMI 55 47 51 beforeWL 76 47.5 60 kg after

18 months treatment rmetHuLeptin(0.01-0.04 mg/kg) daily evening

Polygenic obesity

Challenge Discover pertinent genes, gene combinations and interactions

Rare monogenic mutation

LEPR, POMC, PCSK1SIM1, LEP, others

Increase

d energy

INS-VNTR

MC4R

HNF1A

LPLHSL

PPARG

mtDNA

ADRB3

GYS

UCP1

Decre

ased

ener

gy ex

penditu

re

GNB3

APOE

AGT

KCNJ11

MC4R

Methodological caveats A challenge for gene-environment interaction studies

• Power (increased sample size)– Major improvement in the last years (data pooling)

• Multiple testing (statistical result corrected)• Replication (test in independent groups)• Biological validation

– Functional assessment of putative disease-causing variants

– Evidence for pathophysiological role of the implicated gene

Tabor Nat Rev Genet 2002Cardon Nature Rev Genet 2001Freely Associating Nature Genet 1999

Variation in the Variation in the DNADNA

Not reversible

--- C ------ G ---

--- A ------ T ---

--- C ------ G ---

Nakao M. Gene.2001 278:25-31.

Express differently depending on the

combination with the environment

FoodNutrient

Genes

Epigenetic

Complex interactions underlying polygenic obesity

Mutch D & Clement K, Plos Genetics 2006

NutritionExercise Viruses

Social Status

Food Abundance

Peer pressure

PollutionTechnologicalProgress

Psychology

NutritionExercise Viruses

hormonesSocial Status

Food Abundance

Peer pressure

PollutionTechnologicalProgress

PsychologyPsychology

Identifying Disease Genes

Family Based Linkage Studies

Population Based Association Studies

Members of a family affected by the Same disease share Identical disease genes

Distribution of disease alleles is Different between Cases and Controls

Genome wide scan in obesity

Europe• French• Dutch• German• Finn• British• …

North America• Caucasians US• Caucasians from Quebec (Quebec family study)• Mexican & African & Asian Americans • Amish• Pima Indians• Nigerian families

• And others

Clement 2002 From the human obesity gene map

Genome scan in obesity

Alternative approach - Alternative approach - HapMapHapMap

• What is HapMap?

• public resource (www.hapmap.org)

• a catalogue of common (MAF ≥ 0.05) genetic variants that occur in human beings (~1

SNP/1kb)

• genetic data from 4 populations (n = 269) with African, Asian, and European ancestry

• 30 trios of Utah residents with European ancestry from the CEPH collection (CEU)

• Aim

• to provide insight into patterns of genetic variation in the human population

• to guide design and analysis of medical genetic studies

• to increase power and efficiency of association studies to medical traits

Phase II was completed October 2005: > 5.800.000 SNPs

253 QTL / 244 candidate genes (only 22 replicated in 5 independent studies)

Y

1 2 3 4 5 6 7 8

9 10 11 12 13 14 15 16

17 18 19 20 21 22 X

AMERICAN AMISH EUROPEAN AFRICANPIMA INDIANS ASIAN

Polygenic obesity: many loci and over 240 candidate genes

Mutc

h &

Clé

men

t, P

LoS G

eneti

cs 2

006 ;

Ran

kin

en

et

al 2006

2q14.1Near INSG2

GAD2

ENPP1

SLC6A14

FT0

Positional candidates?

• Chromosome Xq24. Suviolahti et al, JCI 2003 found association between obesity and an SNP haplotype in the 3'-untranslated region of SLC6A14, an (amino solute carrier family 6 member 14) acid transporter involved in serotonin synthesis and for SNP haplotypes of the SLC6A14 gene (P = 0.0007-0.006). No recent news about his role or other confirmation

• Chromosome 10 linked locus. Boutin et al, PLOS 2003 : a SNP haplotype, in GAD2, involved in GABA Formation, associated with morbid obesity in French adults. Not replicated in independent population (*4), incl. functional study

• Chromosome 6. Meyre et al. Nature Genet (2005): association between a 3-allele risk haplotype defined by the polymorphisms K121Q, IVS20delT-1, and A-G+1044TGA) and childhood obesity (OR = 1.69), morbid or moderate obesity in adults (OR= 1.50), and type II diabetes (OR = 1.56). ENPP1 is a membrane glycoprotein that inhibits insulin receptor. Not replicated in independent populations

• Chromosome 2. Herbert et al Science 2006 found an association near a SNP upstream the INSIG2 gene associated with common obesity in adults and children.

• Chromosome 16q12. Scott et al, Frayling et all Science 2007 found an association between the fused toes (FT0) gene and obesity in children and adults. Association confirmed by Dina et al Nat. Genet 2007. Large population discussed but gene role unknown. Replication?

• National Heart, Lung and Blood Institute (NHLB1) Framingham Heart Study (FHS), 25y follow-up, heritability 37-54%

• 116,204 SNPs in 694 participants, and 86,604 tested for association with BMI

• Keep the top 10 with the highest power estimate

• Only one associates with BMI. Rs756605: CC have 1 unit BMI over GC OR 1.33 [1.20-1.48]

C Confirmatory analysis in 5 pop

• Rs756605 located 10 kb upstream the ATG of INSIG2 (insulin-induced gene)

• INSIG2 Inhibits fatty acid and cholesterol synthesis

• Overexpression of INSIG2 in liver rat decreases TG levels

• Located in a QTL for obesity in mice

• and humansBut Rs756605 could be in LD

with another gene

Candidate genes in obese populations

Food intake-centralMonoamines, Peptides&receptors : CART, DRD2, NPY, NPYR, MC3R, POMC, HT2A, AGRP, MC3R, MC4R

Food intake-peripheralPancreatic peptides; Isl1, CCK receptors A&B, GLP1-R

Thermogenesis AR1, 2, 3, AR, CAPN10UCP1, 2, 3

And others ..

FAT and glucose metabolism leptin, leptinR,insulin, InsR, SUR, PTP1b, IRS1, Isl1, GCK LPL, HSL, GRL, DGAT, CPT-1apoA4, B, E, CD36, FABP2, LDLR, LIPE, GRL, TNF , TNF-R, adiponectinMaster genes ? PPAR, CDX3, SREBP1

49 Negative associations

30 Positive associations

Morbid obesityLife span Weight gain

Obesity onsetFat mass

Glucid valuesLipid valuesFood intake

Physical activity

Risk factors for obesity or related phenotypes

Gene Phenotype Odd ratios (risks)3-AR (Trp64Arg)* High weight gain 1.7 (Clément, 1995)

UCP1 (-3826 A/G)* High weight gain 1.4 (Clément, 1996)

UCP1+ 3-AR High weight gain

In morbid obesity

3-4 (Clément, 1996)

GAD2 (risk haplotype) Morbid obesity 1.30 (Boutin, PLOS, 2003)

PTP1b (risk haplotype) Obesity

dyslipidemia

1.49 (Coudreau, 2004)

SREBP (risk haplotype) Morbid obesity

Diabetes

dyslipidemia

1.53 (Eberlé, 2004)

SLC6A14 (risk haplotype) Obesity 1.27-1.35 (Boutin, 2004)

ENPP1 (risk haplotype) Diabetes 1.37 (Meyre et al, 2005)

PPAR(Pro12Ala) Diabetes 1.5-1.6* (meta-analysis)

hundreds

Thousands

FTO gene obesity 1.22-1.67* (3 studies)

(38,759 participants)

Polygenic Individual combination in

interaction with environmental factors

Rare Monogenics1 gene 1 disease

LEP, LEPR, POMC,PCSK1

SIM,,

Increased energ

y intake

INS-VNTR

MC4R

HNF1A

inSig SNPFT0

PPARG

ENPP1

ADRB3

GYS

UCP1

Decre

ase

ener

gy ex

penditu

re

GNB3

APOE

AGT

KCNJ11

MC4R

Future ChallengeGenes x genes interaction

Profile Risk for agiven phenotype ?Protective profile

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24

Ratio:polyunsaturated fatty acids

Saturated fatty acids

25

26

27

≤0.39 ≤0.51 ≤0.66 >0.66

PPARGPPARG ProPro12 12 AlaAla

IMC

(Luan et al 2001 Diabetes 50:686)

Genes/macromolecules Nutrients

Provided by Pr C Junien

Physical activity- Genotype InteractionRole of Adrenergic receptor 2: Gln27Glu

28

27

26

25

24

100

98

96

94

92

90

88

p < 0.0001 ns

p < 0.0001 ns

Without Withphysical activity

Gln27Gln

Glu+/- and +/+

BMI

Waist

Meirhaeghe Lancet 1999Provided by C Junien

Hormone- physical activity- gene interactionRole of Guanine nucleotide binding protein GNB3 C825T

T allele

C allele

Provided by C Junien

Common variant/common disease hypothesis Unsolved questions?

• Are there common genetic factors specific to obesity?• What is the influence of common disease-influencing alleles

when they are in other genetic backgrounds, in other genetic combinations, influenced by other epigenetic or environmental factors (and how to study them)?

• If these susceptibility genes are not causative and modify obesity risk in a certain context, what are they doing in the meantime. Are they neutral or deleterious for other diseases?

• Do they have subtle effects in other epigenetic or environmental contexts?

Adapted from Becker Medical hypothesis, 2004

• Obesity phenotypes (insulin sensitivity) • Liver diseases• Asthma • Psoriasis• Coeliac disease• Chronic Bronchitis• Colitis

Example: TNF (G/A –308) functional variant

Adapted from Becker Medical hypothesis, 2004

Positive association

Identify key molecular drivers of human obesity Challenging Mission ?

• Gene cloning strategies improve– High density maps (Hapmap)– SNP mapping (blocks)– New strategy of analysis in very

large populations (SNP mapping)

• « Omic strategies »– Genomic– Transcriptomic

– Proteomic – Metabolomic

• Combined strategies

U872

30,000genes

300,000proteins

3,000metabolites

Toward integration of knowledge

Data bases

Large scale expression

13

21

6

14

22 Y

17

45 7

910

11

19

31 2

8

12 15 16

18 20X

**

Genetic map Animalmodels

New targets?

other« Omic »

Computational biology

U872

LOCAL

Agriculture/market

Care

Security

Transport

Foodindustry

Prevention

Modified from Ritenbaugh C, Kumanyika S, Morabia A, Jeffery R, Antipatis V. IOTF website 1999: http://www.iotf.org

POPULATION

%

OBESE

SCHOOLWORK, etc

Activities

Infection

Work

Food

Leisure

Family

INDIVIDUAL

Energy exp

FoodEnergydensity

NATIONAL/ REGIONAL

Education

Food

Urbanisation

Health

Social sec’ty

Transport

Media &Culture

INTERNATIONAL

Development

Globalisation

Media

A multitude of interacting factors…..

Strategy and tool transitionG

ene

s

Experiments

0.2 -0.7 -0.2 -0.7 1.2 -0.4 -0.6 -0.5 -0.6-0.9 -0.6 0 -0.4 -1.1 -0.8 -1.6 -2 -0.5 -0.4-0.8 -0.6 0.1 -0.3 0.2 0 -0.6 -0.9 -0.4 -0.4-0.2 -0.7 -0.3 -0.2 0.2 -0.4 -0.9 0.2 0-0.6 -0.5 -0.8 -0.7 -0.7 -0.4-0.2 -0.1 -0.1 -0.5 -0.8 0 -0.6 -0.2 -0.4 0.9

-1.5 -0.3 -0.3 -0.2-0.1 0 -0.1 0 0 0.3 0.6 0.1 0.3 -0.3

0.3 -0.4 -0.5-0.1 -0.5 -0.1 0.1 -0.7 0.2 -0.4 -0.3 -0.6 -0.1-0.4 -0.6 -0.5 -0.6 -1.5 -0.9 -0.8 -0.6 -0.4 -0.4-0.7 -0.3 0.4 0.1 0.1 0.2 -0.6 -1 -0.1 -0.2

-0.4 -0.4-1.1 -0.9 -0.3 -0.4 -0.3 -0.8 -0.3 -0.5-0.7 -0.6 -0.3 -0.3 -0.5 -0.5 -0.2 -0.4 0.3 -0.4-1.5 -0.7 0.3 -0.6 -0.7 -0.6 -0.4-0.5 -0.9 0.3 -0.4 0.3 0.4 -0.6 -0.8 -0.5 -0.2-0.2 -0.2 -0.1 -0.2 -0.9 -0.6 -0.6 0.3 -1.2 -1.1

1 0.6 1.1 0.7 0.4 0.5 0.9 1 1 0.1-0.1 -0.2 -0.3 -0.2 0.1 0.3 0.1 0.4 1 0.8-0.5 -0.8 -0.1 0.2 0 0.6 -0.8 -0.6 -0.1 0.2-0.6 -1 0.3 -0.2 1.7 -0.6 -0.9 -0.4 -0.4-0.5 -0.6 -0.7 1.3 -0.6 -0.3-0.1 -0.8 -0.6 -0.7 -0.3 -0.8 -0.2 -0.5 0.4 -0.2

0 -0.6 1 -1 -1.7 -0.4 -0.1-0.8 0.4 -0.6 0.7 -1 -0.6 -0.4-0.6 -0.9 -0.9 -1.3 -0.3-0.5 -0.6 -0.1 0.4 0 -0.4 -0.7 -0.5-0.9 -0.8 -0.8 0.3 1.2 -0.6 -1.1 -0.6 0.1

-0.7 -1 -0.4 -0.5-0.6 -0.7 -0.9 -0.8 -0.7 0 -0.8 -1 0.2 0.2-0.3 -0.6 -0.6 -0.5 0.5 -0.6 -0.6 0.2 -0.2-1.2 -0.9 0.5 -0.9 -0.8 -0.6 -0.2

-1 -0.8 0.6 -0.8 -1.2 0 -0.5-0.4 0.6 0.1 0 1.3 2.9 0 0.7 0 2.30.3 0.2 -0.5 1.5 -0.1 0.1 -0.8 -0.31.3 -0.8 -0.1 -0.3 -0.3 -0.5 2 1.8 1.9 0.1

-0.1 -0.5 -0.7 -0.1 0 0.9 0.9 -0.30.3 1.1 -0.2 -0.2

-0.7 -1.2 0.6 -0.6 -0.8 -0.4 0.11.2 0.4 0.5 0.3 0.1 0.5 1.3 1.1 0.1 0.2

-0.6 -0.6 -0.3 0.2 0.3 1 -0.1 -0.8 0.7 -0.2-0.8 -0.1 0 -0.4 -0.2 0.9 -1.1 -0.9 -0.5 -0.1-0.1 -0.3 -0.6 -0.3 -0.3 0.1 0.3 -0.2 -0.4

0 -0.7 -0.1 -0.1 -0.8 -0.4 -0.6 0.1 0.20 -0.6 0.6 0.4 -0.1 0 0 0 0.4 -0.7

-0.6 -0.6 -0.7 0.3 1.2 -1.2 -0.9 -0.3 -0.10.5 -0.3 0.4 0.1 -0.1 0.1 0.3 0.1 1.2 00.5 0.5 0.5 0.4 0.5 0.4 0.4 0.6 0.1 0.4

0 -0.6 0.3 -0.1 -0.3 -0.4 0.2 -0.6 0.3 -0.3-0.9 -0.7 0.9 1 -0.8 -0.7 -0.3 -0.1-0.7 -0.6 0.1 0.9 -0.3 -0.4 -0.4 -0.3-0.6 -0.6 -0.6 -0.1-0.7 -0.9 -0.4 0.7 0.5 -0.6 -0.5 0.3 -0.5

0 -0.5 -0.7 -0.5 -0.9 -0.5 -0.5 -0.9 0.2 -0.4-2.5 -0.4 0.1 -0.3

0.1 -0.7 -0.4-0.2 -0.5 0.2 0.2 -0.1 -0.5 0 -0.4-0.3 -0.5 -0.2 -0.3 -0.2 -0.4 0.1-0.5 -0.6 0.6 -0.2 -0.6 -0.5 -0.8 -1.2 -0.2 -0.2-0.1 -0.2 0 -0.1 0 0.6 -0.2 -0.5 -0.6 -0.20.3 0.8 0.4 0.3 -0.1 0.6 0.5 -0.6 -0.5

0 -0.4 -0.1 -0.2 0 -0.5 0.3 -0.1 0 -0.21.1 0.1 0 -0.4 0.2 0.3 0.1 -0.2 0

-0.3 -0.3 -0.4 -0.2 -0.1 -0.2 -0.8 0.1 -0.2-0.3 -0.4 -0.5 -0.7 -1.8 -0.5 -0.6 -1 -0.5 -0.20.8 0 -0.7 -0.6 -1.5 -0.7 0.7 0.2 1.3 0.2

-0.5 -1 0 -0.5 -0.5 -0.1-0.5 -0.3 -0.4 -0.2 0 0.1 -1.2 -0.1 -0.4-0.9 -0.2 1.6 -0.4 -0.5 -1.8 -1

The better the tools become, the clearer the picture…..

Obesity map : a sisyphean task

Abbreviations Abbreviations used Iused I

AC Acetylcholine

ACTH Adrenocorticotropic hormone

AGRP Agouti related peptide

ARC Arculate nucleus

BBS Bardet-Biedl syndrome

BDNF Brain-derived neurotrophic factor

CEPH Centre d’Etudes du Polymorphisme Humain

CLIP corticotropin-like intermediate lobe peptide or ACTH18-39

CPE Carboxypeptidase E

CPH Carboxypeptidase H

CTX Collagen fragment peptide AHDGGR

Dpd Deoxypyridinoline (bone resorption marker)

EcoR1, BspE1 Restriction enzymes

GFP Green fluorescent protein

GHR Ghrelin receptor

GLP Glucagon-like peptide

Gs, Gi, Go Guanine binding proteins (s = stimulating, I = inhibiting)

IBD Identical by descent

IFT Intraflagellar transport

IL Interleukin

IR Insulin receptor

Abbreviations Abbreviations used IIused II

LepR Leptin receptor

LOD Logarithmic odds

LPH Lipotropic pituitary hormone

M Mutant

MC4R Melanocortin4 receptor

MSH (α-, etc) Melanocyte stimulating hormone

N Normal

NIe Normal

NPY Neuropeptide Y

PC (1, etc) Prohormone convertase

POMC Pro-opiomelanocortin

PPARG Peroxisome proliferative activated receptor, gamma

PVN Paraventricular nucleus

PYY Pancreatic Peptide YY3-36

RMR Resting metabolic rate

SIM1 Drosophila single-minded gene

SNP Single nucleotide polymorphism

SSCP Single strand conformation polymorphism

TDT Transmission disequilibrium test

TKRP Tachykynin-related peptide

Z-score Number of standard deviations from an age/sex adjusted mean