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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
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
LVIVAIA
N
K
N
LSCI
LLTIIIT
ESGN
SVSVLMD
AVA
FFY
DNVIDS
VICSSLL
ASI CSLL
SIA
DRYF
F
TI
ITMFFTM
LALMASL
YVHM FLMA RL
H
I
K
R
I
IG
SV TCAA WIC S
III GVRK V
T
LFFP A
WCV
VFVGIL ITLT IAGK MN
A GQRI
L
N
Y
A
LFNL
YLILIMCNS
IIDPLIY
A
HS
PM
S
T T
V
NI
AL Q Y H
N
M
I
II
SS
Y
D ASV
I
ICL
V L PG
T
A
G
C P
QN
P Y CV
C
F
MSH
Y
P
N
S VF L
E
A
S HL R Y S S
QF
R
S
Q
E
L
R
K
T
F
K
E
I
I
CC
L
P
GL
L
G
CDLSSRY
HLWNR
GMHT
SL
VNSTHR M
K
G
GL
S
E
S
C
Y
G
G
D
S
Y
DST
F
QAD
ILH
SIYF
5
249
10
15
20
25
151
131
120
127
70
63
42
80
90
97
105
137
145 163
174
168
195
179
211
253
242
260
281
298
55
185
267
235
201
216
30
35
40
K
V
100
290
308
312
320
H
S
H LC
F*
M
C
S
M
L
ID
T
P
L
T
D
I
P
WQ
--
VT
P
S
E
I
S
S*
Y
S
P
H
T
W
S
T
Q
A
V*
S
L
K
T
S
R
K
VL
L
C
R
N
S
S
N
R
NH2
COOH
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
50,00
52,00
54,00
56,00
58,00
60,00
62,00
64,00
66,00
68,00
70,00
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
U872
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
U872
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