Transcript No Slide Title

Genetics of Cardiovascular
Diseases
Jacques Genest MD
Cardiovascular Genetics Laboratory
McGill University Health Center
Genetics loads the gun, environment
pulls the trigger
Elliott Joslin
Age is a major cardiovascular risk
factor
Framingham Heart Study
The older I get, the better I was
A Cowboy
Human Biochemical Genetics 2009
Genetics of Cardiovascular Diseases
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General Principles
Historical Aspects
Monogenic Disorders
Genome-wide Association (GWA)Studies
Mendelian Randomization
Epigenetics
Genetics of CAD
 Monogenic Disorders
 Rare, extremes traits
 Candidate genes association studies
 Biased, often not replicated
 Genome-wide scan associations
 Unbiased, weak clinical relevance
Genetics of CAD
Watkins et al. Nature Reviews Genetics
published online 07 February 2006
Genetics and CAD
Genetics of CAD is complex.
Family Hx of premature CAD increases
risk > 2.0 fold
 <55 for father; <65 for mother
 Corrected for other RF
 Association weaker in INTERHEART (case
ascertainment of familial CAD weaker than in
FHS).
Lloyd-Jones D et al. Lancet 2004;291:2204
Genetics and Survival
Genes
Environment
0
50
Age
100
General Principles
Chromosomes and DNA
Types of Genetic Disease
Single Gene (Mendelian) Disorders- e.g. sickle cell disease,
familial hypercholesterolemia, cystic fibrosis
Multifactorial or Complex Diseases- e.g. diabetes, asthma,
heart disease
-Family/Twin/Adoption Studies
Chromosomal Disorders- e.g. trisomy 21 (Down syndrome),
XO Turner syndrome
Copy Number of Variant Repeats
Nature
23 Nov 2006
Genetics of Complex Traits
Historical Aspects
Cholesterol Synthesis Pathway
Istvan E and Deisenhofer J. Science 2001;292:1160-1164
Risk Factors for CAD
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Cigarette
Hypertension
LDL-cholesterol (apo B)
HDL-cholesterol
Diabetes
Age
Atherosclerosis
Circulation 2000;101:111-116
INTERHEART: Conclusions
Risk Factor
OR
Population Attributable
Risk
35.7%
Smoking
2.87
Apo B/AI
3.25
49.2%
Hypertension
1.91
17.9%
Diabetes
2.37
9.9%
Abd. Obesity
1.62
20.1%
Fruits / Vegetables
0.70
13.7%
Alcohol
0.91
6.7%
Physical Activity
0.86
12.2%
Monogenic Disorders
Genetics of Complex Traits
Case 1
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Familial
Hypercholesterolemia
Heterozygous
Frequency 1:500 (up
to 1:80 in Lac St-Jean)
Tendinous xanthomas
LDL-Receptor gene
defect
LDL-C 2x ULN
Case 2b
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Familial
Hypercholesterolemia
Homozygous
Very rare (1:106)
Premature CAD in
childhood
Extracorporeal LDL
removal
Familial Hypercholesterolemia
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•
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•
Most frequent genetic disorder associated with
premature CAD (3-5%) of patients.
LDL-receptor defects underlie the majority of
cases
CAD develops in men 35-55 years, in women 4565 years.
Respond to statins (+ bile acid binding resins) (+
intestinal cholesterol absorption inhibitors
ezetimibe)
Cholesteryl Ester
O
R C O
Within intestinal cells (and other body cells) some of the
absorbed cholesterol is esterified to fatty acids, forming
cholesteryl esters.
(R = fatty acid chain)
The enzyme that catalyzes cholesterol esterification in plasma is
LCAT (Lecithin:Cholesterol Acyl Transferase) and intracellularly, ACAT (Acyl CoA: Cholesterol Acyl Transferase).
HO
Cholesterol
LCAT
Cholesteryl Ester
O
Triglycerides
O
H2C
O
C
O
O
R1
HC
O
C
O
R2
H2C
O
C
R3
triacylglycerol
H2O
H2C
O
HC
O
H2C
C
O
R1
C
R2
O
 O
C
R3
OH
1,2-diacylglycerol
Lipoprotein Lipase
fatty acid
Phospholipids
CH3
CH3-N-CH3
CH2
CH2
O
-
Phosphate
O=P O
O
- -
CH2 CH CH2
O=C
O
C=O
R2
O
R1
Glycerol
Acyl Chains
(Fatty acids)
Choline
Apolipoprotein
Phospholipid
Triglyceride
Cholesterol
Cholesteryl ester
0.95VLDL
Density (g/ml)
1.006IDL
CHYLOMICRON
RENNANTS
1.02LDL
1.06HDL2
1.10-
HDL3
1.205
10
20
40
Diameter (nm)
60
80
1000
Lipoprotein Metabolism LDL-R
FFA
Liver
HL
LPL
Exogenous
Pathway
Chylo
Remnant
Chylomicron
ApoA-I, A-II
ApoC-I, C-II, C-III
Phospholipids
Free cholesterol
Intestine
Free
Cholesterol
Peripheral
Cells
HL
Steroidogenic
Cells
X
LCAT
HDL3
Nascent
HDL
HDL2
LDL
Liver
ApoA-I, A-II
ApoC-I, C-II, C-III
Phospholipids
Free cholesterol
X
Tg
CETP
PLTP
CE
LPL
IDL
VLDL
FFA
Endogenous
Pathway
3
Liver
HL
LDL Receptor
Cells take up LDL by receptor-mediated
endocytosis.
The cholesterol in LDL is then used by cells,
e.g., for synthesis of cellular membranes.
The LDL receptor was identified by M. Brown &
J. Goldstein, who were awarded the Nobel prize
for this achievement.
IDL
VLDL
ApoB
ApoE
ApoB
Endosome
ApoE
VLDL-R
LRP
ApoB
LDL-R
LDL
Cholesterol
HMG CoA Red
ACAT
Cholesteryl esters
Fatty acids
sER
Lipoprotein assembly and secretion
Bile acids
VLDL
Hepatic Cell
LDL-R Pathway Animation
Familial Hypercholesterolemia
 LDL-R gene (19p13) (Familial Hypercholesterolemia)
 LDL-Receptor Defects
 Apo B gene (2q23) (Familial Defective apo B)
 Apolipoprotein B Mutations
 PCSK9 (proprotein convertase subtilisin/kexin type 9) (1p32)
 Autosomal Dominant Hypercholesterolemia
 ARH gene (1p35-36.1) (Autosomal Recessive Hypercholesterolemia)
 LDL-R internalization defect
 LDL Overproduction Defects (1q21)(Familial Combined
Hyperlipidemia)
Molecular Causes of Familial
Hypercholesterolemia (FH)
ApoB:
Familial defective Apo B
LDL-R:
Primary familial
hypercholesterolemia
ARH:
Autosomal recessive familial
Hypercholesterolemia
PCSK9:
Proprotein convertase
subtilisin/kexin type 9
500
Apheresis
400
300
200
100
1999
1998
1997
1996
1995
1994
1993
1992
+ Atorvastatin
Mean LDL-C (mg/dL)
Mean LDL-C (mmol/L)
LDL Apheresis
Time (years)
Genest J. NEJM 1999;341:490
PCSK9
Life-long exposure to risk factor:
Principles of Mendelian
Randomization
PCSK9 Gene Mutation
(African-Americans)
Cohen J. et al. NEJM 2006;354:1264
Mendelian randomization.
The effect of life-long genetic
variability of risk factor (exposure) on
the disease process.
HDL
High-Density Lipoproteins
Case: Tangier Disease
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•
Tangier Disease
(Familial HDL Deficiency)
Very rare
Orange tonsils
Hepatosplenomegaly
Neuropathy
Premature CAD
Lymphoid tissue foam
cells (incl. intestinal
mucosa)
Lipoprotein Metabolism: HDL
FFA
Liver
HL
LPL
Exogenous
Pathway
Chylo
Remnant
Chylomicron
1
Free
Cholesterol
ApoA-I, A-II
ApoC-I, C-II, C-III
Phospholipids
Free cholesterol
Intestine
X
HL
Peripheral
Cells
Steroidogenic
Cells
LCAT
HDL3
Nascent
HDL
HDL2
LDL
Liver
ApoA-I, A-II
ApoC-I, C-II, C-III
Phospholipids
Free cholesterol
Tg
CETP
PLTP
CE
4
LPL
IDL
VLDL
FFA
Endogenous
Pathway
3
Liver
HL
Nascent HDL
Lipid-free apo AI
ABCA1
Endosome
ApoB
LDL-R
LDL
LCAT
Cholesterol
HMG CoA Red
ACAT
sER
Cholesteryl ester Stores
HDL3
ABCA1
NH2-
 Full-transporter
 Phospholipid and
(cholesterol) efflux to
apoA-I
 Early HDL maturation
 LxR/RxR
apoA-I
- COOH
cholesterol
&
phospholipid
ATP
ATP
ADP+Pi
ADP+Pi
HDL Biogenesis
HDL-C Mass
ABCA1
ApoAI
Liver 80%
ABCA1
ABCG1
Macrophage <5%
Intestine 20%
ABCA1
ApoAI
ApoE
ABCA1 is Essential for HDL Biogenesis
LxR/RxR
ABC Transporters and Human Disease
HUGO
Gene
Disease
Function
ABCA1
ABC1
Tangier / FHD
PL, Chol transport
Sufractant Deficiency
PL transport
ABCA3
ABCA4
ABCR
Stargardt Disease
Rod receptors
ABCB4
MDR3
Familial Intrahepatic Cholestasis 3
Biliary PL secretion
ABCB7
ABC7
X-linked sideroblastic anemia
Iron transport
ABC11
BSEP
Familial intrahepatic cholestasis 2
Bile acid transport
ABCC2
MRP2
Dubin-Johnson Syndrome
Biliary secretion
ABCC6
Pseudoxanthoma elasticum
ABCC7
CFTR
Cystic Fibrosis
Electrolyte transport
ABCC8
SUR1
Persistent hyperinsulinemic hypoglycemia
Insulin secretion
ABCD1
ALD
X-linked adrenoleukodystrophy
Fatty acid
ABCD3
PMP70
Zellweger syndrome
Peroxysome formation
Sitosterolemia
Sitosterol transport
ABCG5,8
ABCB3
TAP2
HSV infection
ABCA1 Mutations
HDL-C is Highly Heritable
 Studies in twins (n=9)
 Family studies (n=14)
 Heritability of HDL-C 0.24 – 0.83
 Canadian data: 0.58
Peackock JM ATVB 2001;21:1823
Candidate Gene Sequence Variants
in Low HDL subjects
 Cohen JC et al. Science 2004;305:869
• ABCA1 variants seen in ~10% of low HDL-C (p<0.001)
 Frikke-Schmidt R et al. J Clin Invest. 2004;114:1343
• Genetic variation in ABCA1 contributes to HDL-C (~10%)
 Alrasadi M et al. Atherosclerosis 2006
• ABCA1 mutations found in 20% of French Canadians with
HDL deficiency.
ABCA1 gene variations in subjects with defective cellular lipid efflux
R219K P312P
42G>T
RDU
5’ UTR
43/45%
1
3
4
5
26G>A
2520C>A
2522C>A
6
7
8
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
L158L
289-291
R219K G316G DCTC
3
4
5
14369T>C
6
7
8
9996-8
DGTT
24T>A
V771M
L158L
270insG
R219K P312P
4152DA
G616V 24T>A
18T>C
8539C>T
8995G>A
7420DT
7792C>T
794DA Q2210H
18T>C
889G>C
UTR
2
3
4
5
6
7
8
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
452DT 24T>A
I883M
23G>A
fs F1840L,
L1869X
30G>T
3
4
5
6
7
8
7792C>T
9936DA 8539C>T
9996-8DGTT 8995G>A
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
3
4
5
7420DT
8241T>A
8995G>A
9936DA
30G>T
6
7
8
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
8995G>A
9620G>A
R1587K
30G>T
3
4
5
6
7
8
7420DT
8549DT
8850T>G
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
ABCA1 mutations found in 20% of
French Canadians with HDL <5%
exon
coding variant
intron
non coding variant
Homozygous variant
not sequenced
gene defect
translation affected
3’
50
UTR
2
3’
50
UTR
2
3’
50
UTR
2
3’
50
8995G>A
1258G>C
splice site
NL-12 5’ UTR
89/59%
1
N1800H
R1587K
30G>T
14369T>C
LBO
5’ UTR
54/66%
1
R1587K
30G>T
9087T>A
9620G>A
3’
50
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
270insG
GOB
5’ UTR
39/58%
1
794DA
UTR
2
238insG
42G>T
RPH
5’ UTR
68/71%
1
17C>T
UTR
2
14369T>C
238insG
296G>C
SBO
5’ UTR
44/62%
1
R1851X
30G>T
9402G>A
9543G>A
9620G>A
Heterozygous variant
50
3’
Lipoprotein Metabolism
FFA
Liver
HL
LPL
Exogenous
Pathway
Chylo
Remnant
Chylomicron
Intestine
Peripheral
Cells
Free
Cholesterol
ApoA-I, A-II
ApoC-I, C-II, C-III
Phospholipids
Free cholesterol
HL
Steroidogenic
Cells
LCAT
HDL3
Nascent
HDL
HDL2
LDL
Liver
ApoA-I, A-II
ApoC-I, C-II, C-III
Phospholipids
Free cholesterol
Tg
Endogenous
Pathway
CETP
PLTP
CE
LPL
3
Liver
HL
IDL
VLDL
Feces
FFA
Modulators of HDL in Humans
LPL
HL LCAT
EL
{
Extracellular
factors
s-PLA2
CETP
O pre-b
a
PLTP
[nm]
-17.0
SMase
-12.2
-9.5
ApoAI
Cellular
factors
{
a-LpA-I
- 7.1
pre-b1 -LpA-I
SR-BI
Lipases
Gene defects identified in man
ApoA
-I-containing
lipoproteins
ABCA1
Dastani Z et al. Figure 1
Candidate genes and HDL-C
Structural
Receptor/Transport
Lipases
Exchange
Apo AI
ABCA1
Hep Lipase (LIPC)
PLTP
Apo AII
NPC1
LPL
CETP
Endo Lipase
LCAT
S-PLA2
SMAse
The Proprotein convertase
kexin/subtilisin type 5 gene (PSCK5)
affects HDL-C
PCSK5 inactivates Endothelial Lipase (EL) directly
and via ANGPTL3 expression
Iatan I. Circ Cardiovasc Genet 2009 Oct
The PCSK5 gene (302 714 bp) contains 21 exons and is located on chr 9q21.13
PCSK5 gene SNPs
SNP locations in the PCSK5 gene. Schematic representation of the human PCSK5
gene locus showing the exon structure and the location of the 19 variants (bottom panel)
identified through sequencing and the 9 genetic variants associated with HDL-C (upper
panel) identified by genotyping. SNPs in bold are associated with HDL-C with P<0.01.
Locations are based on RefSeq NM_006200.3.
Quantitative Trait Analysis PCSK5 and HDL-C
Chromosome
SNP
Trait
Beta
P-Value
9 rs11144782
HDL
-0.07623
0.002021
9 rs11144766
HDL
-0.06287
0.005061
9 rs1339246
HDL
0.05575
0.01767
9 rs1331384
9 rs11144688
9 rs11144690
HDL
HDL
HDL
0.03717
-0.05339
-0.09334
0.03825
0.03921
0.04026
9 rs1338746
9 rs4745522
HDL
HDL
-0.03619
0.05101
0.04393
0.04487
9 rs2050833
HDL
0.04527
0.04515
9 rs11144782
TRIG
0.5019
0.04878
9 rs11144782
VLDL
0.1686
0.03858
9 rs11144782
APOB
10.72
0.02234
EL Phospholipase
activity
HD
L2
HD
L3
_
EL
HSPG
_
ANGPLT3
+
PCSK5
Loss of function
Endothelial cells
Iatan I et al. Figure 2
The Genetics of HDL
Genome-Wide Scans of Families
Genome-Wide Association Studies
Genome-Wide Scans and HDL-C
The two-point linkage results of the genome wide scan of the Canadian families with low HDL-C when allowing for
heterogeneity. The alpha value for the peak marker of each chromosome is indicated for lod scores > 1.0.
3.0
Chromosome 16,
a0.51
2.5
LOD
LOD
2.0
1.5
3.0
2.5
2.5
LOD
LOD
Chromosome 5
3.0
1.0
0.5
0.0
211 cM
Chromosome 9
LOD
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
3.0
2.5
2.0
1.5
1.0
0.5
0.0
Chromosome 14,
a0.23
3.0
2.5
2.0
1.5
1.0
0.5
0.0
Chromosome 15,
a0.62
126 cM
3.0
2.5
130 cM
3.0
Chromosome 19
Chromosome 20
2.5
2.0
1.5
2.0
1.5
1.0
1.0
1.0
0.5
0.5
0.5
0.5
0.0
0.0
0.0
118 cM
Chromosome 10
182 cM
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
Chromosome 18
1.5
1.5
150 cM
Chromosome 13
2.0
2.0
1.0
3.0
Chromosome 21
Chromosome 8
132 cM
Chromosome 17
133 cM
0.0
113 cM
101 cM
Chromosome 22
2.5
LOD
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
173 cM
131 cM
3.0
2.5
2.0
1.5
1.0
0.5
0.0
Chromosome 12,
a0.31
Chromosome 4,
a0.49
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
154 cM
3.0
2.5
2.0
1.5
1.0
0.5
0.0
3.0
2.5
2.0
1.5
1.0
0.5
0.0
160 cM
LOD
Chromosome 11
LOD
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
Chromosome 7
192 cM
194 cM
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
0.0
209 cM
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
LOD
Chromosome 6
Chromosome 3,
a0.30
225 cM
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
265 cM
LOD
LOD
263 cM
3.0
2.5
2.0
1.5
1.0
0.5
0.0
LOD
3.0
2.5
2.0
1.5
1.0
0.5
0.0
Chromosome 2,
a0.59
LOD
LOD
LOD
Chromosome 1
3.0
2.5
2.0
1.5
1.0
0.5
0.0
2.0
1.5
1.0
0.5
0.0
57 cM
68 cM
Figure 3
A Gene on Chromosome 16 affects
HDL-C levels
WWOX: tumor suppressor gene contains 2 WW
domains and a short-chain dehydrogenase domain
(SRD). Expressed in Sterol producing tissues and in
the liver
D8Mit12
LOD=3.5
MouseQTL
RegionforSNPsassociationinSLSJ(23Mb)
LOD(QTL)=2.3
QUE(95cM)
2.6
1.1 1.1
B
8.1
1.4
CHST6
1.4 0.8
0.8
3.2
0.8
3.2
.6
80.2
1.8
77.7
7.4
62.2
54.9
cen
DiscreteLOD=1.7
QUE(D16S505)
75.1
LOD(QTL)=2.55
SLSJ(85cM)
D
10
tel
A
25.5cM~18Mb
C
18.1cM~7.8Mb
1-1430581
2-27587.2
3-1200242
4-1434384
5-27587.1
6-1435859
7-27413
8-1440369
9-1384255
10-24292
Figure 2
WWOX Protein
 WW domains indicates a role in protein-protein interactions. WWOX binds
the proline-rich domain PPxY.
 Highest expression detected in hormonally regulated tissues such as
testis, ovary, prostate. Expression pattern and presence of SRD domain
suggests a role in steroid metabolism.
 Wwox-/- mice testis and ovaries display impaired gene expression of key
steroidogenesis enzymes.
 Interrogation of several online databases show that WWOX is strongly
associated with HDL-C (P = 0.0000225). [Willer 08]
HDL Biological Networks
PCSK5
PLTP
AGPL4
EL
sPLA2
SMPD1
LPL
ABCA1
Apo E
CETP
HDL-C
HL
?
Apo AI
?
LCAT
SR-B1
ABCG1
?
WWOX
Genetics of HDL:
Family Studies and Candidate Genes
 Several genes account for ~25% of severe
HDL deficiency (HDL-C <5th percentile) i.e.:
 A genetic basis for HDL is identified in 1-2%
of subjects
 New genes (SMAse, PCSK5, WWOX)
provide novel pathways in a complex
network
HDL are More Complex than Imagined
J Clin Invest 2007:117:748
Vaisar, T. et al. J. Clin. Invest. 2007;117:746-756
Copyright ©2007 American Society for Clinical Investigation
Questions?
Second session 21 Jan 2010
Genome-Wide Association Studies
(GWAS)
Katherisan S, Willer C, Nat Genet 2009
Genetics of Complex Traits
The yet identified genes together explain only a small amount of
less than 10% of the HDLC variance, which leaves an enormous room for
further yet to be identified genetic variants.
This might be accomplished by large population-based genomewide meta-analyses and by deep-sequencing approaches on the identified
genes.
The resulting findings will probably result in a re-drawing and
extension of the involved metabolic pathways of HDLC metabolism.
Exp Gerontol 2008
Genome-Wide Scans and
Quantitative traits
Broad and Lund database
Wellcome-Trust Case Control
Consortium (WTCCC)
Framingham Study Database
 Fusion/Sardinia/FHS
Common variants at 30 loci contribute to polygenic dyslipidemia
Sekar Kathiresan, Cristen J Willer et al. Nat Genet 2009;41;36
Common variants at 30 loci contribute to polygenic dyslipidemia
Sekar Kathiresan, Cristen J Willer et al. Nat Genet 2009;41;36
Genes you have seen before in candidate gene approach
Common variants contribute to Lipoprotein Lipid Levels
Cristen J Willer et al. Available on line (www.sph.umich.edu/csg/abecasis/public/lipids/)
GWAS HDL-C Trait
Sekar Kathiresan, Cristen J Willer et al. Nat Genet 2009;41;36
Trait Chrom
SNP
P val
Gene
MAF
Effect (SD)
HDL
11q12
rs174547
2x10-12
FADS1-2-3
T, C (0.33)
–0.09(0.02)
HDL
16q22
rs2271293
9x10-13
LCAT
G, A (0.11)
+0.07 (0.03
HDL
9p22
rs471364
3x10-10
TTC39B
T, C (0.12)
–0.08 (0.03)
HDL
20q13
rs1800961
8x10-10
HNF4A
C, T (0.03)
–0.19 (0.05)
HDL
20q13
rs7679
4x10-9
PLTP
T, C (0.19)
–0.07 (0.02)
HDL
19p13
rs2967605
1x10-8
ANGPTL4
C, T (0.16)
–0.12 (0.04)
HDL
16q13
rs173539
4x10-75
CETP
C, T (0.32)c
+0.25 (0.02)
HDL
8p21
rs12678919
2x10-34
LPL
A, G (0.10)c
+0.23 (0.03)
HDL
15q22
rs10468017
8x10-23
LIPC (HL)
C, T (0.30)c
+0.10 (0.02)
HDL
18q21
rs4939883
7x10-15
LIPG
C, T (0.17)
–0.14 (0.02)
HDL
1q23
rs964184
1x10-12
A1-C3-A4-A5
C, G (0.14)c
–0.17 (0.03)
HDL
12q24
rs2338104
1x10-10
MMAB, MVK
G, C (0.45)
–0.07 (0.02)
HDL
9q31
rs1883025
1x10-9
ABCA1
C, T (0.26)c
–0.08 (0.02)
HDL
1q42
rs4846914
4x10-8
GALNT2
A, G (0.40)
–0.05 (0.02)
Common variants at 14 loci contribute to HDL-C
Sekar Kathiresan, Cristen J Willer et al. Nat Genet 2009;41;36
Based on combined GWAS analysis
of >40,000 subjects, 11% of variance
of HDL-C levels can be explained.
The Genetics of HDL:
Impact on HDL-C or CAD?
 Monogenic Disorders
 Genome-wide Associations
 Association with CAD
Mendelian randomization is a
method of using non-experimental
studies to examine the causal effect
of a modifiable exposure on disease
by making use of measured variation
in genes of known function.
Mendelian Randomization
Implies causality of a gene product
(intermediary phenotype) in a disease
process
Gene
IP
Often used, perhaps wrongfully, to dismiss a gene or its product as a
causal factor
Copenhagen Heart Study: HDL-C
and CVD Risk
Frikke-Schmidt R JAMA. 2008;299(21):2524-2532.
Copenhagen Heart Study: ABCA1
Mutations and CVD Risk
Frikke-Schmidt R JAMA. 2008;299(21):2524-2532.
HDL-C Epidemiology
4.0
Observations:
4.0
3.0
CHD
risk
ratio 2.0
2.0
1.0
1.0
0
0.65
1.17
• Risk of CHD varies
continuously and
inversely with HDL-C
levels.
• CHD risk decreases by
50% for each 0.52
mmol/L increase in
HDL-C (unproven).
1.68
HDL-C (mmol/L)
Kannel WB. AJC 1983;52,9B-12B
HDL Epidemiology: Yin and Yang
4.0
3.0
CV Risk
CHD
risk
ratio
4.0
ABCA1**
2.0
2.0
1.0
0
CETP Deficiency
(▲ CV Risk)
ABCA1*
LCAT
1.0
HL (LIPC)
Apo AI Milano (▼ CV Risk)
0.65
1.17
1.68
HDL-C (mmol/L)
3.16
*Copenhagen Heart Study
** Wellington S, Genest J
Genome-Wide Associations
(GWA) Studies
The Genetics of Complex traits
Genome-Wide Scans of Families
Genome-Wide Association Studies
Genetics of Complex Traits
Genome-Wide Scans for CAD and MI
(Lack of )
Validation of Genetic Markers for CAD
Morgan T et al. JAMA 2007;297:1551
The Genetics of Continuous traits






Heritability
Segregation Studies
Genome-Wide Scans of Families
Quantitative Trait Loci (QTL)
Genome-Wide Association Studies
Mouse Synthenic Regions
Phenotype Distance
Genetics of complex traits: longer
phenotype distance decreases specificity
Lipid Levels
Biol. Pathways
Risk Factor
Biomarkers
IMT
Surrogate
End-Points
CHD death, MI
Mortality/
Morbidity
Phenotype
Distance
Genome-Wide Scans and CAD:
Chromosome 9q21 locus
•
•
•
•
McPherson R. Science 2007;316:1488
Helgdottir A. Science 2007;316:1491
WTCCC Nature 2007;447:661
Samani NJ. NEJM 2007;357:443
• Drinking from the fire hose –Statistical issues in
genome-wide association studies: Hunter DJ. NEJM
2007;357:436
Genome-Wide Scans for CAD and MI
Samani NJ. NEJM 2007;357:443
Chromosome 9q21: which gene?
Meta-analysis of 9p21 and heart disease
Schunkert et al. Circulation 2008
Mendelian Randomization
Women’s Genome Health Study
GWAS for Plasma C-Reactive Protein Level
Am J Hum Genet 2008;82:1185-1192
Mendelian Randomization
CRP Genetics and Outcome
Zacko et al NEJM 2008;359:1897.
Epigenetics
DNA Methylation
DNMTs
• Transcriptional regulation
• Cancer
• Genome stabilization
• ICF, RETT syndrome
• Genomic imprinting
• Prader-Willi, Angelman,
Beckwith-Wiedemann
syndromes
• X-inactivation
Imprinted Genes
Snrpn
Igf2r
DMR1
DMR2
7 CpGs
16 CpGs
Peg1/Mest
Peg3
Promoter & exon 1
Promoter & exon 1
23 CpGs
DNA from 400 oocytes  Bisulfite genomic sequencing
18 CpGs
The Epigenome
Nature 429:457, 2004
Human Diseases Associated with
Altered Methylation Profiles
Cancer
Inactivation of tumor
suppressor genes
Imprinting Diseases
Inactivation of
DNA repair genes
- Angelman Syndrome
- Prader-Willi Syndrome
- Beckwith-Wiedemann
Syndrome
CpG island
hypermethylation
Normal DNA methylation
Global hypomethylation
?
?
?
Chromosome
instability
Retrotransposon
activation
Adapted from Strathdee et al., Expert Reviews in
Molecular Medicine (2002).
Oncogene
activation
ICF Syndrome
Immunodeficiency,
Centromeric region
instability, Facial
anomalies
Mutation in DNMT3B
 hypomethylation
of centromeric
chromatin
Imprinted Genes
Angelman and Prader-Willi syndromes
locus
ZNF217
NDN
SNURFSNRPN
MAGEL2
IC
ZNF217-AS
PAR-SN
15q11-q13
UBE3A
PAR5
PAR1
GABRB3
IPW
GABRG3
GABRA5
UBE3A-AS
Beckwith-Wiedemann syndrome locus
11p15.5
KCNQ1
NAP1L4
TSSC3
TSSC5
CDKN1C
CD81
ASCL2
TH
INS
IGF2
H19
IGF2-AS
KCNQ1OT1
Loss of Maternal Methylation at SNRPN and KCNQ1OT1
WT1
Female Predominance and Transmission
Distortion in the Long-QT Syndrome
Long QT syndrome caused by KCNQ1 and
KCNH2 mutations
Autosomal Dominant
Transmission Ratio 55% Female; 45% Male
(p=0.005 from normal)
 Possible genomic imprinting
Imboden M et al, NEJM 2007;355:2744-2751
EPIGENETICS and CVD
Long-QT syndrome, types 1 and 2, are caused by mutations
in the potassium-channel genes KCNQ1 and KCNH2
Female Predominance and Transmission Distortion in the
Long-QT Syndrome
Imbodem M. NEJM 2006; 355:2744-2751
http://www.mgu.har.mrc.ac.uk/research/imprinting/imprin-viewmaps.html
Human Biochemical Genetics 2009
Genetics of Cardiovascular Diseases






General Principles
Historical Aspects
Monogenic Disorders
Genome-wide Association Studies (GWA)
Mendelian Randomization
Epigenetics