Genetics of obesity
From genetics to functional genomics
Prof. Karine Clément
Inserm U872 Nutriomique
Université Paris 6/Cordelier Research Centre
Endocrinology and Nutrition Dept, Pitié-Salpêtrière
Paris
Karine.clement@psl.aphp.fr
Genetics of obesity
from genetics to functional genomics
Contents of presentation
Slides
Introduction
Monogenic obesity: case study BBS
Other mono- and oligogenic examples
Polygenic obesity: pertinent genes and risk factors
Gene-gene and gene-environment interactions
The future
Abbreviations used
3–5
6 – 21
22 – 41
42 – 57
58 – 63
64 – 69
70 - 71
Obesity: chronic disease with different stages of
development
Epigenetic events
Intervention
weight
Genes_ Environment Interaction
Systemic and signal
Pathology
Constitution
U872
Aggravation
Chronic disease
Resistance/Regain
Complications
years
Obesity: complex physiopathology
Hypothalamus
Afferent Signals
Efferent signals
Ghrelin
PYY
Insulin
Amylin
IL6
Leptin
Adiponectin
Sympathic
Parasympathic
Thyroid Hormones
others
•Hypothesis driven
(candidate gene)
•Hypothesis generating
approach
Genetics of human obesity
Dissection and strategy
Environment
Genes
Monogenic
High penetrance
•Rare cases
•Syndromes
U872
Monogenic
Low penetrance
Variable expression
•Population study
•Genetic epidemiology
Polygenic
•Tissue investigation in clinical trials
• “omic studies”
Example: Adipose tissue analysis
Monogenic forms of obesity
or obesity cases with strong genetic influence
Strategic « choices »
Hypothesis generating
Hypothesis raised
Human Syndromes
Clinical cases
Hypothesis
Genome wide scan
Screening of a known gene
Gene identification
Biochemistry
Genetics
Comparative genomics
Molecular/cellular studies
Physiology
Gene mutation
Novel disease/Novel syndrome
From clinical syndromes to genes
Syndrome Name
(reference)
Clinical
heterogeneity
Transmission
Loci / Genes
Prader-Willi
Muscular Hypotony
Mental retardation
Hyperphagia
Hypogonadism
Short stature
Autosomic
dominant
imprinting
15q11
SRNPN
Micro deletion
Maternal Disomy
Bardet-Biedel
Hypogonadism
Pigmentary retinopathy
Polydactyly
Mental retardation
Autosomic
recessive
BBS (1-12)
chaperonin Protein MKKS
(Chr 20)
Ciliary cells proteins
Myocardiopathy
Sensory deficit
(retinopathy, deafness)
Dyslipidemia, diabetes
Autosomique
recessive
2p14
ALMS1
Mykytyn Nature Genet
2002
Alström
Hearn Nature Genet 2002
Collin Nature Genet 2002
Börjson-Forssman-Lehman
Lower Nature genet 2002
Morbid obesity, epilepsy
Hypogonadism, facial
dysmorphy
Xq26.3 / Plant homeodomain
like finger gene
Bardet-Biedel Syndrome (BBS)
Obesity in
childhood (75%)
Polydactyly
Retinitis pigmentosa
…. And other diseases (uro-genotal anomalies, kidney malformation) and
cognitive dysfunction
Discovered in the late 19th centuries
Known 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
Current Genome scanning approach
Family collections
Microsatellite genotyping
Family
Collection
> 500 subjects Parents & Children
400-800 Markers
Fine Mapping
Many Genes
Loci 15-30 Mb
1 to 2 years (<6 months)
Infrastructure:
Automated Sequencers
PCR machines
Liquid handling robots
Running costs: High
Loci ~ 5 Mb
Extensive
SNP Analysis
Therapeutic
Target
Infrastructure:
Automated SNP system
PCR machines
Liquid handling robots
Thousands of samples
Running cost: High
Linkage analysis
complex disease
Linkagein
analysis
LOD-score analysis
(homozygosity
mapping)
Sib-pair analysis
Tests the cosegregation of
alleles in (large)
non-linkage
Tests the distribution alleles
IBD among affected sib
pairs against H0=1/2
TDT
Tests the transmission of
alleles from hetero-zygous
parents to offspring
against H0=1/2
Qualitative traits
Method of sibling pairs
(principals)
AB
CD
AC
Father AB and Mother CD
The second child could be
Number of identical alleles (IBD)
Proportion of identical alleles (xi)
Probability (pi)
If the first child is AC
AC
AD BC
BD
2
1
0
1
1/2
0
1/4
1/2
1/4
Proportion of alleles IBD =  PIXI = 
Absence of linkage:  = ½. If  ≥ 1/2 test for linkage (t)
?
Quantitative
traits linkage
Quantitative
trait linkage
analysis
analysis in affected Sib-Pairs
Fine mapping strategy in family collections
Linkage with markers
Linkage confirmed
Collection 1
Collection 2
•Increased samples
•Increased markers at locus
•SNP maps, combine haplotypes
• Positional candidate SNP
mapping
• Obese controls studies
• Sib-TDT analysis
3
2
1
M1
M1
M1
1 cM
M1
M1
BBS: 1st surprising result
Multiple genes involved in BBS
*
*
*
* Genome wide scan + comparative genomics
BBS: 2nd surprising result
BBS genes encode unknown proteins or ones related to primary
cilium. It is a model of ciliopathy
Nom
BBS1
Locus
11q13
BBS2
BBS3
BBS4
16q21
3p13
15q22
BBS5
BBS6
2q13
20p12
BBS7
4q27
BBS8
BBS9
BBS10
BBS11
BBS12
14q32
7p14
12q
9q33.1
4q27
Gene
Protein
BBS1
Ciliary protein
(M390R mutation 80%)
BBS2
Ciliary Protein
BBS3
G-ADP ribosylation
BBS4
PCM1 recruitment
(pericentriolar material protein)
BBS5
synthesis cilia flagella
MKKS
McKusick-Kaufman
(chaperonin)
BBS7
Ciliary protein
(close to BBS 1 & 2)
BBS8(TTC8)
Cell Motility (primary cilia)
PTHB1
regulated by Parahormone
BBS10
Chaperonin Protein (new)*
BBS11
? Unconfirmed
BBS12
Chaperonin Protein (new)*
Motile or immotile (primary) cilia are located
on the surface of nearly every cell within the mammalian body
Davenport, J. R. et al. Am J Physiol Renal Physiol 289: F1159-F1169 2005;
doi:10.1152/ajprenal.00118.2005
Copyright ©2005 American Physiological Society
Primary cilia function in tubules as sensors for fluid flow
Dysfunction
of movement
regulation
(BBS7,8)
Davenport, J. R. et al. Am J Physiol Renal Physiol 289: F1159-F1169 2005;
doi:10.1152/ajprenal.00118.2005
Copyright ©2005 American Physiological Society
BBS: 3rd surprising result
In some BBS families there is a triallelic mode of
transmission (genetic epistasis)
BBS4
Heterozygous
BBS1
Homozygous
Phenotype
Adapted from Mutch & Clement, Plos genet 2006
BBS: from syndrome to genes
and 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 »
Hypothesis generating
Hypothesis raised
Human Syndromes
Clinical cases (disease = associated features)
Hypothesis
Genome wide scan
Screening of a known gene
Gene identification
Biochemistry
Genetics
Comparative genomics
Molecular/cellular studies
Physiology
Gene mutation
Novel disease/Novel syndrome
Monogenic obesity affecting the leptin/melanocortin pathway
Human mutations
HYPOTHALAMUS
Paraventricular
Nucleus
Arcuate Nucleus
POMC
LepR
IR
PC1
PC2
+
MC4-R
α-MSH
β-MSH
α-MSH
LepR
IR
GHR
+
NPY
AGRP
β-MSH (?)
+
-
SIM1
?
AGRP
TKRB
BDNF
Ventromedial
Nucleus
Leptin
Insulin
Ghrelin
Adipose
Pancreas
Stomach
tissue
Energy balance
Mutch & Clement, 2006
Morbid obesity in two cousins
Serum leptin concentration (ng ml-1)
Inappropriate leptin levels based on corpulence
examination
Ob1 and Ob2
heterozygote sibling
normal siblings
heterozygote mothers
heterozygote fathers
95% confidence intervals
of the mean
normal children
normal adults
Homozygous G del codon 133
Nature, 387, pp 903-908
June 26, 1997
7q31
cEBP

5’
1
Gene= 18kb
cDNA= 3.5 kb
Leptin
2
10kb
1.9kb
*
167 aa
Leptin* 133aa
*
*
3
AAAA
3’
POMC post-transcriptional processing
NH2
COOH
N-teminal
γ-LPH
γ3-MSH
α-MSH
γ1-MSH
Β-LPH
ACTH
JP
CLIP
β-MSH
β-end1-27
PC1 cleavage site
Hypothalamus products
PC2 cleavage site
Anterior Pituitary products
Modified by Coll et al., 2004
POMC and derived actions
POMC
ACTH
MSH
MSH
ACTH
ss
MC1-R
ss
MC2-R
Eumelanin pigment Synthesis
Skin
MC4-R
Glucocorticoids
Feeding inhibition
Adrenal gland
Hypothalamus
POMC and derived actions
•Compound heterozygous for exon 3 mutation (G->T nt7013 & del at 7133)
•No ACTH and aMSH synthesis
POMC
MSH
ACTH
MSH
(Krude et al, Nature genet, 1998)
ss
MC1-R
ss
MC2-R
Eumelanin pigment Synthesis
Skin
Glucorticoids
Adrenal
MC4-R
Feeding inhibition
Hypothalamus
POMC aberrant proteins in humans
Adapted from Krude, JCEM, 2003
Mutation of Proconvertase 1
O’Rahilly et al, NEJM, 1995 &Jackson et al, Nature Genet 1997, Jackson, Nat Genet 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
Fraction Number
Normal Pathways of Processing and effects of the Putative Defect in
Prohormone Convertase 1 in the Study Patient
Leptin and melanocortin mutations
Food intake
Energy expenditure
Mice
Humans
Ob
Db
5*
POMC-/-
3*
Rare syndromes
Adapted from D Cummings, 2003
6*
fat
1*
Mc4r (-/-)
?
Obesity only
Obese phenotype
Extracellular
More than 90 mutations in MC4R gene…..
2-3% obesity cases
20
25
A
N
S
H
L
R
Y
S
S
R
N W
15
L
H
L
10
S
T
H
M
30
5
G
S
C
E
H
S
H
L
A
F*
L
R
NH2
M
T
S N
V
S
G
H
K
G
35
Y
L
S
S
V*
D
Y
G
P
G
M
C
40
T
Y
S
T
D
A
Q
S
T
F
V
S
Y
120
P
N
K
T
S
Q E 42
D
R
I
D
S
S
A
V
I
I
195
C
C P
267
F
Y
C
V
Q
I
185
Y
I
S
L
I
F
N
H S
M
281
H
I
L C
I N
L N
L
V
260
N F
N D
I
L F
L
105 T L
T
I
V
F F
M
Y
P
P S
V
L
G
I
F
290
P
I
A
I L
201
L
F
L
I I
E
R
W
127 S D
179 V S
T
T
V
C
T
M
V
I
V F
E 100
M
V
S*
I
C
C
C
H
A L
T
131
N G S
A A
D
F V
P
55 G L
N
W 174
M L
253 V
S
S S
S
S
G
L
I
97
V
A
I
C
I
S
L
I
C
S V
I
L I
S
L S
T
I
L S
A
211
I
249
T
Y
L V
V
D 298
L
I S
L
V
I
R
P
C
M
E
137
K
L
T
N
D
M H
Q
I
S
168 I
216
G
63 I
T
90
L L
L F
G A
R V
V A
Y I
L
K
S
V
A
S
K
242
M
I
A
M
V 163
A I
L
N
145 -S
L R
A
V
A
312
V
S
C
A
T
A I
I
D
Q G
F
T
Y R
70
K
H
I R
F
T I
N
L
N
F
Y
235
Q W
80
T
T
I
M
M
A
151
E
I
305 R L F I
P
K
M
I
F
S R K C
G
S
T
K
N
Y
N L H
C
I
Q K E C
H
A
T
320
R
L Q Y
Y
E
L
W
G
I
A V L P
D
P
308
L
P
S
G
S
G
L
L
C
D
Y R S S L
S
F
L
Intracellular
COOH
70,00
Early weight gain
68,00
66,00
in children with MC4R mutations
64,00
LepR
62,00
Mutation
60,00
58,00
56,00
(French children)
54,00
52,00
50,00
U872
48,00
P97
46,00
LepR
44,00
P95
Mutation
LEPR mutation
IMC
42,00
P90
40,00
38,00
MC4R homozygote ( AG 346-347)
P75
36,00
P50
34,00
32,00
MC4R homozygote (I166V)
P25
30,00
P5
28,00
97P
26,00
Homo (V166I
24,00
MC4R heterozygote children (13)
22,00
50P
20,00
LepR 2
18,00
Obese children with wild type MC4R (40)
LepR 1
16,00
Non mutes
14,00
Het MC4R
12,00
10,00
0
Clement Nature 1998 ; Dubern, et al J Pediatr 2001 and 2007
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15 16 17 18
Age (ans)
Functional consequences of MC4R mutations
Data from the French population
AGRP
N
Membrane expression
MSH
-
Intracellular retention
=> 56% of MC4R mutations
+
C
X
Prot Gs
AC
AMPc
?
Food Intake
Energy
homeostasis
Lubrano-Berthelier et al, HMG 2003
Srinivasan et Lubrano-Berthelier et al JCI 2004
Lubrano-Berthelier et al, JCEM 2006
Receptor activity
Deficit of MSH response
80% of MC4R mutation
Decreased basal activity
=> 76% of MC4R mutations
Genotype-phenotype Relationships
Intracellular retention associated with early onset
obesity
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)


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)




Review in Govaerts Peptide 2005
Finland (Valli-Jaakola, JCEM 04)
France (Lubrano, Dubern, Clément Vaisse,
Italy (Miraglia Del Giudice, JIO 02, Buono 05)
Spain (Marti IJO 03)
Switzerland (Branson, NEJM 03)
Denmark (Larsen, JCEM 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 adults
homozygous Cys105Thr (Licino, PNAS, 2004)
C
Y
40
BMI 55
WL 76
B
35
47
47.5
A
27
51 before
60 kg after
18 months treatment rmetHuLeptin
(0.01-0.04 mg/kg) daily evening
Rare monogenic
mutation
Polygenic obesity
Challenge Discover pertinent genes, gene combinations and
interactions
KCNJ11
APOE
GNB3
AGT
HSL
ADRB3
MC4R
PPARG
UCP1
INS-VNTR
LEPR, POMC, PCSK1
SIM1, LEP, others
MC4R
LPL
mtDNA
HNF1A
GYS
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 2002
Cardon Nature Rev Genet 2001
Freely Associating Nature Genet 1999
Food
Nutrient
Genes
Variation in the DNA
Epigenetic
--- C ----- G ---
--- C ----- G ----- A ----- T ---
Express differently
depending on the
combination with the
environment
Not reversible
Nakao M. Gene.2001 278:25-31.
Complex interactions underlying polygenic obesity
Exercise
Viruses
Nutrition
hormones
Social Status
Peer pressure
Food
Abundance
Technological
Progress
Pollution
Psychology
Mutch D & Clement K, Plos Genetics 2006
Identifying Disease Genes
Family Based Linkage
Studies
Members of a family affected by the Same disease
share Identical disease genes
Population Based
Association Studies
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
•
Clement 2002
And others
From the human obesity gene map
Genome scan in obesity
Alternative approach - HapMap
• 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
Polygenic obesity: many loci and over 240 candidate genes
253 QTL / 244 candidate genes (only 22 replicated in 5 independent studies)
2
5
6
7
13
14
15
16
Y
X
ENPP1
8
GAD2
9
17
10
18
11
19
12
20
21
22
FT0
Mutch & Clément, PLoS Genetics 2006 ; Rankinen et al 2006
1
2q14.1
3
Near INSG24
SLC6A14
AMERICAN
AMISH
EUROPEAN
PIMA INDIANS
AFRICAN
ASIAN
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?
•
•
•
•
C Confirmatory analysis in 5 pop
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]
• 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 humans
But Rs756605 could be in LD
with another gene
Candidate genes in obese populations
Food intake-central
Monoamines, Peptides&receptors :
CART, DRD2, NPY, NPYR, MC3R, POMC, HT2A,
AGRP, MC3R, MC4R
Thermogenesis
bAR1, 2, 3,  AR, CAPN10
UCP1, 2, 3
FAT and glucose metabolism
leptin, leptinR,insulin, InsR,
SUR, PTP1b, IRS1, Isl1, GCK
LPL, HSL, GRL, DGAT, CPT-1
apoA4, B, E, CD36, FABP2, LDLR, LIPE,
GRL, TNF , TNF-R, adiponectin
Master genes ? PPARg, CDX3,
SREBP1
Food intake-peripheral
Pancreatic peptides; Isl1, CCK
receptors A&B,
GLP1-R
Morbid obesity
Life span Weight gain
Obesity onset
Fat mass
Glucid values
Lipid values
Food intake
Physical activity
And others ..
30 Positive associations
49 Negative associations
Risk factors for obesity or related phenotypes
Gene
Phenotype
Odd ratios (risks)
b3-AR (Trp64Arg)*
High weight gain
1.7 (Clément, 1995)
UCP1 (-3826 A/G)*
High weight gain
1.4 (Clément, 1996)
UCP1+ b3-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)
PPARg (Pro12Ala)
Diabetes
1.5-1.6* (meta-analysis)
FTO gene
obesity
1.22-1.67* (3 studies)
(38,759 participants)
hundreds
Thousands
Rare Monogenics
1 gene 1
disease
Polygenic
Individual combination in
interaction with environmental
factors
KCNJ11
APOE
GNB3
AGT
FT0
inSig SNP
ADRB3
MC4R
PPARG
HNF1A
UCP1
ENPP1
INS-VNTR
LEP, LEPR,
POMC,PCSK1
SIM,,
MC4R
GYS
Future Challenge
Genes x genes interaction
Profile Risk for a
given phenotype ?
Protective profile
U872
Genes/
macromolecules
Nutrients
PPARG
Pro12 Ala
27
26
IMC
25
24
≤0.39
≤0.51
≤0.66
>0.66
polyunsaturated fatty acids
Ratio:
Saturated fatty acids
Provided by Pr C Junien
(Luan et al 2001 Diabetes 50:686)
Physical activity- Genotype Interaction
Role of Adrenergic receptor b2: Gln27Glu
28
p < 0.0001
ns
27
BMI
26
25
Gln27Gln
24
100
p < 0.0001
ns
98
Waist
Glu+/- and +/+
96
94
92
90
88
Provided by C Junien
Without
physical
With
activity
Meirhaeghe Lancet 1999
Hormone- physical activity- gene interaction
Role 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
Example: TNF (G/A –308) functional variant
Positive association
•
•
•
•
•
•
•
Obesity phenotypes (insulin sensitivity)
Liver diseases
Asthma
Psoriasis
Coeliac disease
Chronic Bronchitis
Colitis
Adapted from Becker Medical hypothesis, 2004
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
300,000
proteins
3,000
metabolites
30,000
genes
Toward integration of knowledge
Data bases
Genetic map
Large scale expression
*
1
9
17
*
2
10
18
5
4
3
11
19
12
20
6
13
21
7
14
15
22
Y
Animal
models
8
16
X
Computational biology
U872
New targets?
other
« Omic »
A multitude of interacting factors…..
INTERNATIONAL
Globalisation
NATIONAL/
REGIONAL
LOCAL
SCHOOL
WORK, etc
Transport
Transport
Leisure
Urbanisation
Security
Work
Health
Care
INDIVIDUAL
POPULATION
Energy
exp
%
Infection
OBESE
Development
Social sec’ty
Media
Media &
Culture
Prevention
Food
Food
Energy
density
Food
industry
Family
Agriculture/
market
Activities
Education
Food
Modified from Ritenbaugh C, Kumanyika S, Morabia A, Jeffery R, Antipatis V. IOTF website 1999: http://www.iotf.org
Strategy and tool transition
The better the tools become, the clearer the picture…..
0.2
-0.9
-0.8
-0.2
-0.6
-0.2
-0.7
-0.6
-0.6
-0.7
-0.5
-0.1
-0.2
0
0.1
-0.3
-0.7
-0.4
-0.3
-0.2
-1.1
0.2
-0.1
-0.1
-1.5
-0.1
-0.5
-0.8
0
0
-0.1
-0.4
-0.7
-0.5
-0.6
-0.3
-0.1
-0.5
0.4
0.1
-0.6
0.1
0
0.3
-0.7
-1.5
0.1
-1.1
-0.7
-1.5
-0.5
-0.2
1
-0.1
-0.5
-0.6
-0.5
-0.1
0
-0.8
-0.6
-0.5
-0.9
-0.9
-0.6
-0.7
-0.9
-0.2
0.6
-0.2
-0.8
-1
-0.3
-0.3
0.3
0.3
-0.1
1.1
-0.3
-0.1
0.3
-0.6
-0.6
-0.4
-0.3
-0.6
-0.4
-0.2
0.7
-0.2
0.2
-0.2
-0.7
-0.7
0.4
-0.9
-0.6
-0.9
-0.1
-0.6
-0.3
-1.2
-1
-0.4
0.3
1.3
-0.7
-0.6
-0.9
-0.8
0.6
0.2
-0.8
-0.1
-0.7
1.2
-0.6
-0.8
-0.1
0
0
-0.6
0.5
0.5
0
-0.9
-0.7
-0.6
-0.7
0
-2.5
-1.2
0.4
-0.6
-0.1
-0.3
-0.7
-0.6
-0.6
-0.3
0.5
-0.6
-0.7
-0.6
-0.8
-0.6
Genes
-0.6
-0.8
-0.2
-0.3
-0.5
-0.1
0.3
0
1.1
-0.3
-0.3
0.8
-0.5
-0.5
-0.9
-0.9
-0.5
-0.4
-0.5
-0.5
-0.6
-0.2
0.8
-0.4
0.1
-0.3
-0.4
0
-0.3
-0.8
-0.7
-0.9
-0.6
0.1
-0.5
-0.1
-0.5
0.6
0.5
-0.3
0
-0.6
-0.1
0.6
-0.7
0.4
0.5
0.3
-0.8
-0.5
0
-0.7
0.1
0.2
-0.2
0.6
0
0.4
-0.1
0
-0.4
-0.5
-0.7
-1
-0.4
-0.2
-0.5
0.4
-0.6
0.5
0.3
0.6
1.7
1.3
-0.8
1
0.7
-0.3
0.4
0.3
-0.7
0.5
0.6
1.3
0.3
0.2
-0.4
-0.3
-0.1
0.4
0.1
0.3
-0.2
-0.3
-0.8
-0.1
0.3
-0.1
0.5
-0.3
0.9
0.9
-0.4
-0.5
0.2
-0.9
0.2
0.3
-0.9
0.4
0.1
0
-0.3
-0.1
0.3
0.1
-0.6
0
-0.3
0.3
-0.5
-0.3
-0.7
0.1
0.4
-0.1
1.2
-0.8
0
0.2
1.2
0
0.5
2.9
1.5
-0.5
0
1.1
0.5
1
0.9
0.1
0
1.2
0.1
0.4
-0.4
1
0.7
-0.9
0.5
-0.5
-0.2
-0.1
0.3
-0.2
-0.4
-0.2
-0.7
-0.6
-0.6
0
-0.1
0
-0.5
0.6
-0.2
0
0.2
-1.8
-1.5
-0.5
0.2
-0.1
-0.5
-0.7
0
0.1
1.6
-0.4
-1.6
-0.6
-0.4
-0.8
-0.6
-0.6
-2
-0.9
-0.9
-0.7
-0.2
0.6
0.1
-0.4
-0.8
-0.6
-0.3
-0.6
-1
-0.3
-0.2
-0.7
-0.6
-0.6
0.9
0.1
-0.8
-0.6
-0.8
-0.4
-0.2
-1
-1
-0.5
-1.7
0
-0.6
-1
-0.8
-0.6
-0.9
-0.8
0
-0.1
2
0.9
-0.4
-1.1
-0.6
1.3
-0.1
-1.1
0.3
-0.4
0
-1.2
0.3
0.4
0.2
-0.8
-0.3
-0.8
1.1
-0.8
-0.9
-0.6
-0.5
-0.5
-0.9
-0.1
-0.3
-0.8
-0.2
0.6
0.3
0.3
-0.2
-0.6
0.7
-0.5
-1.2
-0.4
-0.5
-0.2
-1.2
-0.5
0.5
-0.1
0.1
-0.8
-1
0.2
-0.8
0.3
1
0.4
-0.6
-0.9
-1
-0.6
-0.8
-1.2
0.7
0.1
1.8
-0.6
0
-0.9
0.1
0.6
-0.6
-0.7
-0.4
-0.5
Experiments
-0.5
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0.2
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-0.1
-0.4
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0.3
-0.6
-0.5
-1.2
1
1
-0.1
-0.4
-0.6
0.4
-0.4
-0.6
-1.3
-0.7
-0.6
-0.4
0.2
0.2
-0.6
0
0
-0.8
1.9
0.9
-0.2
-0.4
0.1
0.7
-0.5
-0.2
0.1
0.4
-0.3
1.2
0.1
0.3
-0.3
-0.4
-0.6
0.3
0.2
0.1
-0.7
0
-0.4
-0.2
-0.6
-0.6
0
-0.2
0.1
-0.5
1.3
-0.5
-0.1
-1.8
-0.6
-0.4
-0.4
0
-0.4
0.9
-0.2
-0.3
-0.5
-0.1
-0.4
-0.2
-0.4
-0.5
-0.4
-0.4
-0.2
-1.1
0.1
0.8
0.2
-0.4
-0.3
-0.2
-0.1
-0.4
-0.3
-0.5
0.1
-0.5
0.2
-0.2
-0.2
-0.5
2.3
-0.3
0.1
-0.3
-0.2
0.1
0.2
-0.2
-0.1
-0.4
0.2
-0.7
-0.1
0
0.4
-0.3
-0.1
-0.3
-0.1
-0.5
-0.4
-0.3
-0.4
-0.4
0.1
-0.2
-0.2
-0.5
-0.2
0
-0.2
-0.2
0.2
-0.1
-0.4
-1
Obesity map : a sisyphean task
Abbreviations
used 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
used 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