BCVS July, 2010
“Systems Genetics of
Cardiovascular Disease”
Jake Lusis, UCLA
BCVS July, 2010
“Systems Genetics of
Cardiovascular Disease”
Jake Lusis, UCLA
“The goal of Systems Biology is to identify all
the elements of a system and to construct a
network that explains their interactions”
No conflict of interest to declare
Problem
• It is clear that atherosclerosis is a
chronic inflammatory disease.
However, the mechanisms that
initiate and propagate inflammation
are poorly understood.
Atherosclerosis and Inflammation
IL-8
Adhesion
Molecules
Oxidized LDL induces expression of
inflammatory genes in endothelial cells
Rajavashisth et al. Nature 1990
Oxidized Phospholipids Have Many
of the Pro-Inflammatory Properties
of Oxidized LDL
Low Density Lipoprotein
Bioactive Phospholipids and Ox-PAPC
O
O
O
O
OP
O
O
OH
H
O
O
O
O
O
OP
ON
O
OH
O
O
O
O
OP
ON
O
OH
OH
O
O
HO
O O
O
O
O
OP
ON
O
OH
+
+
+PAPC
POVPC
PGPC
PEIPC
N+
Ox-phospholipids accumulate in the sub-endothelial
space of human atherosclerotic lesions(EO6 antibody specific for oxidized phospholipids)
Genetic Background Determines Responses to
Oxidized Lipids in Mouse Endothelial Cells
Shi et al. , Circ. Res.. 2000
B6.ApoEB6.ApoE--//-- C3H.ApoEC3H.ApoE--//--
2525
2020
1515
1010
55
00**
Aort
ic L
esio
ns
Aort
ic L
esio
ns
DONOR HAEC #
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
IL8
(p
g/m
l)
0
200
400
600
800
1000
1200
1400
oxPAPC
PAPC
Evidence of genetic differences affecting
responses to oxidized phospholipids in human EC
Early passage primary human aortic endothelial cells (HAEC) were isolated from
heart transplant donars
87 genes
70
17
Bacterial LPS (2 ng/ml)oxPAPC (50 ug/ml)
742 genes
459
283
Major Differences in Gene Regulation Between
LPS and OxPAPC
vs.
22 genes
17 5
COMMON GENES
Unfolded Protein Response genes are induced in
human atherosclerotic lesions
ATF3 EO6
Human aortic EC
Gargalovich et al (2006)
Goal of study
• There is strong evidence that oxidized
phospholipids contribute in part to the
initiation and propagation of
inflammation in atherosclerosis.
However, the pathways involved are
poorly understood. We sought to
obtain a systems-level view of
endothelial cell inflammation.
Systems Biology
1. Define the system.
2.Identify the components of the system.
3. Construct a network that explains the
interactions of the components.
Systems Biology
1. Define the system. Cultured human aortic
endothelial cells
2. Identify the components of the system.
3. Construct a network that explains the
interactions of the components.
Systems Biology
1. Define the system. Cultured human aortic
endothelial cells
2. Identify the components of the system.
Transcripts responsive to OxPAPC treatment
3. Construct a network that explains the
interactions of the components.
Systems Biology
1. Define the system. Cultured human aortic
endothelial cells
2. Identify the components of the system.
Transcripts responsive to OxPAPC treatment
3. Construct a network that explains the
interactions of the components. Use
naturally occurring variation in the
population that results in hundreds of
perturbations affecting gene expression
Systems genetics uses naturally occurring variations
in a population to perturb the “system” and examine
the interactions among its “elements”.
Yellow
Module
Turquoise
Module
A mouse liver gene network
Graphs: A collection of nodes
(dots) and edges (links)
Nodes: Elements of the
system under study (the dots)
Edges: Relationship between
elements of the system (the
links)
Biologic networks
1 2 3 162
Control
Ox-PAPC
RNA RNA RNA RNATranscript Levels(Affymetrix HT-HU133A)
~20,000 transcripts
Human Aortic
Endothelial
Cells (HAEC)
Genotyping(Affymetrix Hu SNP 6.0)
~1 million SNPs
DNA DNA DNA DNA
0 20 40 60 80
Donor
Basal Transcript Expression Levels Vary in Primary Endothelial Cell Cultures
10
9
8
7
6
5
4
AT
F3 m
RN
A E
xpre
ssio
n
(log
2in
tensity)
Donors Ranked by ATF3 Basal Gene Expression
control
OxPAPC
OxPAPC-Responses Vary in Primary Endothelial Cell Cultures
0 20 40 60 80
Donor
10
9
8
7
6
5
4
AT
F3 m
RN
A E
xpre
ssio
n
(log
2in
tensity)
Donors Ranked by ATF3 Basal Gene Expression
control
OxPAPC
OxPAPC-Responses Vary in Primary Endothelial Cell Cultures
0 20 40 60 80
Donor
10
9
8
7
6
5
4
AT
F3 m
RN
A E
xpre
ssio
n
(log
2in
tensity)
Donors Ranked by ATF3 Basal Gene Expression
control
OxPAPC
OxPAPC-Responses Vary in Primary Endothelial Cell Cultures
0 20 40 60 80
Donor
10
9
8
7
6
5
4
AT
F3 m
RN
A E
xpre
ssio
n
(log
2in
tensity)
Donors Ranked by ATF3 Basal Gene Expression
control
OxPAPC
Constructing a gene network
slide courtesy of Steve Horvath, UCLA
Individuals 1 2 3 4 5 …………….....
1200 nodes from HAEC network generated
using Ox-PAPC regulated genes.
Genes are colored by “module”
Casey Romanoski
Peter Gargalovich
Todd Kirchgessnerand colleagues (BMS)
Judy Berliner
Thank You!
Sangderk LeeImran MungrueMete Civelek
