Transcript Chan, Timothy1, MacAulay, Calum2, Lam, Wan2 , Lam, Stephen2 ,... University of British Columbia, Vancouver, Canada

Chan, Timothy1, MacAulay, Calum2, Lam, Wan2 , Lam, Stephen2 , Lonergan, Kim2 , Ng, Raymond2.
University of British Columbia, Vancouver, Canada
BC Cancer Agency, Vancouver, Canada
Overview
 Fold change of CIS/Normal average expression must be > 10
The 5-year survival rate of an advanced
lung cancer patient is only about 10%.
 Fold change of CIS/Normal average expression must be > 5
If the cancer is caught early at the CIS
(carcinoma in situ) stage, the 5-year survival
rate is 90%.
 Fold change of CIS/Metaplasia average expression must be > 2
 Permutation score > 2.35 for both sets (p-value of 0.01)
 Currently, there are no studies have
isolated biomarkers for this elusive CIS
stage.
Results
We propose using lung SAGE data to isolate genes specific for CIS stages of
lung cancer that are not present in bronchial metaplasia tissue.
 After applying the above criteria we obtained 18 tags.
 14 had unigene ids and 11 mapped to genes with names.
Objective
Top 18 Filtered Tags
 To determine whether these genes are good candidate biomarkers from a
biological stand point.
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Met Avg
100
CIS Avg
INV Avg
80
Other desmosome families of the armadillo proteins (PKPs) and
plakins were also found to be higher expressed (refer to boxplots).
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20
0
TT
C
AG
C
C
CT
T
G
G
Tag Name
Methodology
DSC2
20
15
10
5
0
AD
V
AV -00
E13
37
Br
W
1
Br
W
2
Br
-JA
Br
-S
S
27 SAGE
25
B
CS rR
-1
1
C S 94
-1
4
D D 54
-1
73
8
LP
-0
0
RW
-1
6
S K 72
-1
52
4
SK
-1
68
2
Me TF00
t-S
A_
CI
l on
Sg
JA
_lo
CI
ng
S_
K_
CI
lo
S_
RW ng
_l
CI
S_ ong
R_
CI
l
S_ ong
W
_
SQ long
-A
_
SQ long
-B
_l o
Inv
ng
-S
S_
lon
g
Inv
Inv
W
_K
_lo
Inv
ng
_P
_lo
ng
Raw Gene Expression
To conduct our experiment we used 1 metaplasia
library, 15 smoked-damaged (normal) libraries, 6
invasive libraries, and 5 CIS libraries.
Library
DSG3
1. A calcium-dependent
glycoprotein that is a
member of the desmocollin
subfmaily of the cadherin
superfamily
2. Found primarily in
epithelial cells where they
constitute the adhesive
proteins of the
desmosome cell-cell
junction anad are required
for cell adhesion
CIS
Normal
Invasive
Raw Gene Expression
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CIS
 Desmocollin 2 and desmoglein 3 are major components of cell
adhesion molecules which play an important role in epithelial adhesion.
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TA
A
 To discover whether the expression level of these genes associated genes lead
to the understanding of the inner workings of the early stages of the disease.
200
TA
AG
C
TC
TG
CT
G
G
AG
AG
AT
G
C
C
AT
AT
G
AT
G
T
C
AT
AG
TT
AT
C
C
C
AG
AG
AG
G
AG
TC
AT
A
C
CC
TG
TT
TA
T
AA
AT
G
TA
G
AT
TT
TT
AA
AC
AC
CC
CA
G
T
AA
CC
C
AG
G
T
G
G
TA
TT
G
TA
G
C
C
CA
TT
C
A
TG
AA
G
AT
G
T
AT
TC
AA
CA
TT
G
G
G
CG
AA
Raw Expression Count
 To find a set of candidate genes that are highly expressed in the CIS stages
and lowly expressed in normal tissues, metaplasia tissues, and invasive tissues.
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1. A calcium-binding
transmembrane
glycoprotien component
of desmosomes in
vertebrate and epithelial
cells.
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80
60
40
20
 Squamous cell carcinoma cells overxpressing desmosomal cadherins
have been shown to inhibit invasion.
 Othere genes involved include ones involved in EGFR trafficking,
phosphatase genes, and a tyrosine kinase receptors.
 All the genes were looked up on NCBI’s EST database to find where
they are expressed. All these genes were found to be expressed in
various tissues.
Conclusion
 From our results we were unable to find a clear biomarker found that
was exclusive to its tissue type (that is only found or produced by lung).
 Our study on the mRNA levels of the intercellular adhesion molecules
suggest that when a squamous lung cell enters the early stages of lung
cancer, adhesion genes are up regulated.
PERMUTATION TEST
PERMUTATION TEST
B
CS rR
-1
19
4
CS
-1
45
4
DD
-1
73
8
LP
-0
RW 0
-1
6
S K 72
-1
52
4
SK
-1
68
2
T
M
Fet
-S 00
A_
CI
l
S - ong
JA
_l
CI
S _ ong
K
CI
_l
o
S_
RW ng
_l
CI
on
S_
g
R_
CI
lon
S_
g
W
_
SQ lon
g
-A
_l
o
SQ
n
-B g
_l
on
In
vSS g
_lo
ng
In
vW
In
v_
K_
lon
In
g
v_
P_
lon
g
AD
V
AV -00
E13
37
Br
W
1
Br
W
2
Br
-J
A
Br
-S
S
0
Library
2. A member of the cadherin
cell adhesion molecule.
 As it enters the invasive stages, we hypothesize that these cancer
cells have obtained the ability to obtain its own nutrients and thus do not
need to anchor onto bronchial epithelial tissues.
 Interestingly, oral squamous cell carcinoma cells overexpressing
desmosomal cadherins have been shown to inhibit invasion.
*NOTE: pink box is the best mapped tag*
Top 2000 Ranked
Top 2000 Ranked
Future Directions
 Biological validation involving protein expression is required for our
above hypothesis as SAGE only looks at the cell at the mRNA level.
 Analysis of other pathways involving the other set of genes need to
done.
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 It would be also interesting to look at the genes that are turned off or
down-regulated in CIS stages but abundantly expressed in normal and
invasive stages.