the molecular diversity of luminal a breast tumors · the molecular diversity of luminal a breast...
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The molecular diversity of Luminal A breast tumors
Giovanni Ciriello Computational Biology, MSKCC
TCGA Annual SymposiumWashington DC, 2012
Breast'Cancer'Heterogeneity
Breast Cancer Intrinsic Subtypes'
Breast Cancer'
Her2-negative
Her2 - positive PAM50: Her2-enriched
ER - negative PAM50: Basal ER-positive
PAM50: Luminal B
PAM50: Luminal A'
Breast'Cancer'Heterogeneity
Breast Cancer Intrinsic Subtypes'
Breast Cancer'
Her2-negative
Her2 - positive PAM50: Her2-enriched
ER-positive
ER - negative'PAM50: Basal'
PAM50: Luminal B'
PAM50: Luminal A'
Breast'Cancer'Heterogeneity
Breast Cancer Intrinsic Subtypes'
Breast Cancer'
Her2-negative
Her2 - positive PAM50: Her2-enriched
ER - negative PAM50: Basal ER-positive
PAM50: Luminal A
PAM50: Luminal B PAM50 (Perou et al., 2000)
Luminal(Heterogeneity
Integrated data from:
TCGA 2012, Ellis et al. 2012, Banerji et al. 2012 Curtis et al. 2012 Russnes et al. 2010
~ 1500 Luminal tumors
Copy Number Alterations Somatic Mutations mRNA expression
Luminal(Molecular(Heterogeneity
Integrated data from:
TCGA 2012, Ellis et al. 2012, Banerji et al. 2012 Curtis et al. 2012 Russnes et al. 2010
~ 1500 Luminal tumors
Copy Number Alterations Somatic Mutations mRNA expression
IC10
IC5
IC3
IC1
IC4
IC8
IC7
IC9
IC6
IC2Normal
LumB
LumA
Her2
Basal
CNA1
CNA3
CNA2
CNA5
CNA4
Cur
tis d
atse
tTC
GA
dats
et
p < 1010 < p < 0.05
- 4- 4
PAM50 vs CNA-clusters (Curtis et al., TCGA)
Luminal(Molecular(Heterogeneity
Integrated data from:
TCGA 2012, Ellis et al. 2012, Banerji et al. 2012 Curtis et al. 2012 Russnes et al. 2010
~ 1500 Luminal tumors
Copy Number Alterations Somatic Mutations mRNA expression
IC10
IC5
IC3
IC1
IC4
IC8
IC7
IC9
IC6
IC2Normal
LumB
LumA
Her2
Basal
CNA1
CNA3
CNA2
CNA5
CNA4
Cur
tis d
atse
tTC
GA
dats
et
p < 1010 < p < 0.05
- 4- 4
Somatic Mutations (TCGA, Ellis et al., Banerji et al)
CNA-clusters (Curtis et al., TCGA)
0 20 40 60 80
# of mutations per sample # of SigGenes ( q<0.05)
Her2-enriched
Basal-like
Luminal B
Luminal A
Luminal(A(Clinical(Heterogeneity
Luminal A tumors have heterogenous outcome •
METABRIC Dataset (Curtis et al.)7
0 20
00
4000
60
00
8000
Day
s at d
eath
Haque et al., 2012
Basal Her2 LumB LumA
Luminal(Heterogeneity
Luminal A tumors have heterogenous outcome •
Haque et al., 2012
0 20
00
4000
60
00
8000
Day
s at d
eath
METABRIC Dataset (Curtis et al.)
Basal Her2 LumB LumA
Can we link outcome variability to molecular diversity? Luminal A is molecularly and clinically heterogeneous
d
a
b
c
i
h
f
g
B)
e
Chromosomes
A) Luminal A Breast Tumors (TCGA Dataset)
Months Survival
% S
urvi
ving
C)Overall survival (Curtis Dataset)
0 50 100
020
4060
8010
0
Copy Number Quiet1q/16qChr.8-associatedMixedCopy Number High
Overlall Log-rank p = 0.015CNH Log-rank p = 0.001
150
0
10%
20%
30%
40%
50%1q
/16q
Cop
y N
umbe
r Q
uiet
Cop
y N
umbe
r H
igh
Chr
.8as
soci
ated
Mix
ed
T C T C T C T C T C
T: TCGA dataC: Curtis data
%S
ampl
es
Figure 1
*
* **
*
IGP p-value < 0.001*
Luminal(A(Heterogeneity
Copy Number Alterationsidentify five major subgroups
d
a
b
c
i
h
f
g
B)
e
Chromosomes
A) Luminal A Breast Tumors (TCGA Dataset)
Months Survival
% S
urvi
ving
C)Overall survival (Curtis Dataset)
0 50 100
020
4060
8010
0
Copy Number Quiet1q/16qChr.8-associatedMixedCopy Number High
Overlall Log-rank p = 0.015CNH Log-rank p = 0.001
150
0
10%
20%
30%
40%
50%1q
/16q
Cop
y N
umbe
r Q
uiet
Cop
y N
umbe
r H
igh
Chr
.8as
soci
ated
Mix
ed
T C T C T C T C T C
T: TCGA dataC: Curtis data
%S
ampl
es
Figure 1
*
* **
*
IGP p-value < 0.001*
Luminal(A(Heterogeneity
Genomic(Instability(correlates( with(poor(prognosis
A) B) CNH survival (Curtis et al.) CNH Survival (Russnes et al.)
0 20
40
60
80
10
0
% S
urvi
ving
0 20
40
60
80
10
0
% S
urvi
ving
CNH Others Log-rank p = 4.6E-05
0 2 4 6 8 10 12 14,
Years Survival,
CNH Others
Log-rank p = 0.003
0 2 4 6 8 10 12 14,
Years Survival,
Genomic(Instability(correlates( with(poor(prognosis
A) B) CNH survival (Curtis et al.) CNH Survival (Russnes et al.)
0 20
40
60
80
10
0
% S
urvi
ving
0 20
40
60
80
10
0
% S
urvi
ving
CNH Others Log-rank p = 4.6E-05
0 2 4 6 8 10 12 14,
Years Survival,
CNH Others
Log-rank p = 0.003
0 2 4 6 8 10 12 14,
Years Survival,
What are the molecular features of these tumors?
A)
8q.24AURKACDC25BCCNA2AURKB
CDK1CCNA1BIRC5 PLK1
AURKA
PLK1
CDC25B/C
Mitosis
CDK1Cyclin-A/B
C)
Copy Number HighHighLow
Diff
eren
tially
Exp
ress
ed G
enes
B)
TP53BP1POLH
POLI
MLH3POLK
0%
10%
20%
30%
40%
50%
60%
TP53
(mut) MYC
(amp) 20
q
(gain)
5q
(loss
)PIK
3CA
(mut)
Copy Number HighOtherp < 0.01p < 0.05
Luminal A
Luminal A Samples
**
*%Sa
mpl
es
*
**
**
****
CNH$Molecular$Features
CNH$Molecular$Features
What characterizes the other Luminal A subtypes?
A)
8q.24AURKACDC25BCCNA2AURKB
CDK1CCNA1BIRC5 PLK1
AURKA
PLK1
CDC25B/C
Mitosis
CDK1Cyclin-A/B
C)
Copy Number HighHighLow
Diff
eren
tially
Exp
ress
ed G
enes
B)
TP53BP1POLH
POLI
MLH3POLK
0%
10%
20%
30%
40%
50%
60%
TP53
(mut) MYC
(amp) 20
q
(gain)
5q
(loss
)PIK
3CA
(mut)
Copy Number HighOtherp < 0.01p < 0.05
Luminal A
Luminal A Samples
**
*%Sa
mpl
es
*
**
**
****
Somatic mutations
PIK3CA
GATA3
AKT1
MAP3K1
TP53
CNA-Quiet 1q/16q Chr.8-associated CNH Mixed
MA
P3K
18p
11
Chr. 8 Chr.16Chr. 8 - associated
Chromosomes
Sam
ples
MissenseSplice-siteIn Frame Del.NonsenseFrame-shift#m
utat
ions
MAP3K1 mutated samples
Mutation Type
MAP3K1 mutations
A)
B)
0
5
10
15
20
25
1q/16q Quiet Chr.8 CNH Mixed0
5
10
GATA3 Hotspots (e4-2 , P409fs)1q/16q Quiet Chr.8 CNH Mixed
#mut
atio
ns
GATA3MAP3K1PIK3CA
1p12
1q21
1q32
3p25
.14p
16.3
4q13
.36p
236q
276q
14.2
7p12
8q24
.21
8p21
.38p
11.2
28p
11.2
19p
2110
p13
10q2
2.3
10q2
311
p13
11p1
5.5
11q1
3.2
11q1
412
q15
12p1
3.3
13q1
213
q14.
214
q13
14q2
415
q26.
316
q12
16q2
316
q24.
217
p12
17p1
1.2
17q1
217
q21
19q1
219
q13
20p1
320
q13.
221
q11.
2
Co-occurrent (p<0.05)Mutually Exclusive (p<0.05)
Copy Number LossCopy Number Gain
C)
D)
E)
Samples
Mutated genes
CN
A
PIK3CA Mutations GATA3 Mutations
PIK3CA Hotspots (E545K, H1047R/L) Other
Somatic mutations Amplification
Luminal(A(Somatic(Mutations
Somatic mutations
PIK3CA
GATA3
AKT1
MAP3K1
TP53
CNA-Quiet 1q/16q Chr.8-associated CNH Mixed
MA
P3K
18p
11
Chr. 8 Chr.16Chr. 8 - associated
Chromosomes
Sam
ples
MissenseSplice-siteIn Frame Del.NonsenseFrame-shift#m
utat
ions
MAP3K1 mutated samples
Mutation Type
MAP3K1 mutations
A)
B)
0
5
10
15
20
25
1q/16q Quiet Chr.8 CNH Mixed0
5
10
GATA3 Hotspots (e4-2 , P409fs)1q/16q Quiet Chr.8 CNH Mixed
#mut
atio
ns
GATA3MAP3K1PIK3CA
1p12
1q21
1q32
3p25
.14p
16.3
4q13
.36p
236q
276q
14.2
7p12
8q24
.21
8p21
.38p
11.2
28p
11.2
19p
2110
p13
10q2
2.3
10q2
311
p13
11p1
5.5
11q1
3.2
11q1
412
q15
12p1
3.3
13q1
213
q14.
214
q13
14q2
415
q26.
316
q12
16q2
316
q24.
217
p12
17p1
1.2
17q1
217
q21
19q1
219
q13
20p1
320
q13.
221
q11.
2
Co-occurrent (p<0.05)Mutually Exclusive (p<0.05)
Copy Number LossCopy Number Gain
C)
D)
E)
Samples
Mutated genes
CN
A
PIK3CA Mutations GATA3 Mutations
PIK3CA Hotspots (E545K, H1047R/L) Other
Somatic mutations Amplification
Luminal(A(Somatic(Mutations
Somatic mutations
PIK3CA
GATA3
AKT1
MAP3K1
TP53
CNA-Quiet 1q/16q Chr.8-associated CNH Mixed
MA
P3K
18p
11
Chr. 8 Chr.16Chr. 8 - associated
Chromosomes
Sam
ples
MissenseSplice-siteIn Frame Del.NonsenseFrame-shift#m
utat
ions
MAP3K1 mutated samples
Mutation Type
MAP3K1 mutations
A)
B)
0
5
10
15
20
25
1q/16q Quiet Chr.8 CNH Mixed0
5
10
GATA3 Hotspots (e4-2 , P409fs)1q/16q Quiet Chr.8 CNH Mixed
#mut
atio
ns
GATA3MAP3K1PIK3CA
1p12
1q21
1q32
3p25
.14p
16.3
4q13
.36p
236q
276q
14.2
7p12
8q24
.21
8p21
.38p
11.2
28p
11.2
19p
2110
p13
10q2
2.3
10q2
311
p13
11p1
5.5
11q1
3.2
11q1
412
q15
12p1
3.3
13q1
213
q14.
214
q13
14q2
415
q26.
316
q12
16q2
316
q24.
217
p12
17p1
1.2
17q1
217
q21
19q1
219
q13
20p1
320
q13.
221
q11.
2
Co-occurrent (p<0.05)Mutually Exclusive (p<0.05)
Copy Number LossCopy Number Gain
C)
D)
E)
Samples
Mutated genes
CN
A
PIK3CA Mutations GATA3 Mutations
PIK3CA Hotspots (E545K, H1047R/L) Other
Somatic mutations Amplification
Luminal(A(Somatic(Mutations
Which pathways are most de-regulated?
30.5%
8% 8.5%Gene CGene B
Gene D
Gene A54%
t
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MEMo:%Mutual%Exclusivity%Modules
Mutations CNA User Defined Set
Cases
Gen
es
Altered
BRCA1
C24
Q1756
●
●
Homdel Hetloss DiploidGain AmpMutated Normal
Genes connected by network proximity
Not Altered.
Genes Samples
G S
t t + 1
G S G S
MCMC Switching Permutation - preserves #alterations per sample - preserves #alterations per gene
Module
Mutual Exclusivity Module Ciriello et al., Genome Res. 2012 www.cbio.mskcc.org/memo
Luminal(A(Pathways((MEMo)
A)2
PTEN 6%
NF1 3%
IGF1R ERBB2
4% 4%
AKT1 4%
PAK1 8% MAP2K4
11%
KRAS 1%
MAP3K1 14%
PIK3CA 49%
PIK3R1 2%
MAP2K3/6 MAP2K1/2
JNK p38 ERK
Survival Apoptosis Proliferation
Inhibiting interactionActivating interaction
Inactivating Activating
Alterations+to+NCor/SMRT+components
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
Hom. Del
Somatic mutation
Fingerprint
HighLow
mRNA Heatmap1q/16qCopy Number QuietChr.8-associatedCopy Number HighMixed
CNA - Clusters
Alterations+to+NCor/SMRT+components
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
Hom. Del
Somatic mutation
Fingerprint
HighLow
mRNA Heatmap1q/16qCopy Number QuietChr.8-associatedCopy Number HighMixed
CNA - Clusters
Why are co-repressor complexes important in ER+ tumors?
NCor/SMRT*are*required* for*Tamoxifen*effects
Co-repressors
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
Hom. Del
Somatic mutation
Fingerprint
HighLow
mRNA Heatmap1q/16qCopy Number QuietChr.8-associatedCopy Number HighMixed
CNA - Clusters
ER Tamoxifen
Proliferation
NCor/SMRT*are*required* for*Tamoxifen*effects
ER
Co-repressors
Tamoxifen
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
Hom. Del
Somatic mutation
Fingerprint
HighLow
mRNA Heatmap1q/16qCopy Number QuietChr.8-associatedCopy Number HighMixed
CNA - Clusters
ER
Co-activators
Tamoxifen
Proliferation
Loss$of$NCor/SMRT$predicts$resistance
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
NCOR1NCOR2GPS2
ANKRD11TBL1XR1
ER
Co-repressors
Tamoxifen
ER
Co-activators
Tamoxifen
Proliferation
N-Cor
NCOR1 5%
2%
TBL1XR1
2%
GPS2
3%
ANKRD11
p160/SRC
Hom. Del
Somatic mutation
Fingerprint
HighLow
mRNA Heatmap1q/16qCopy Number QuietChr.8-associatedCopy Number HighMixed
CNA - Clusters
ER
NCOR2 1%
SMRT
Proliferation
Conclusions
We dissected the genomics of Luminal A tumors in multiple datasets to explain their molecular and clinical heterogeneity
Four major subtypes of Luminal A tumors
Atypical Luminal subtype characterized by: high genomic instability
p53 mutations Aurora kinases up-regulation poor prognosis
• • • •
Luminal A hallmark mutations are prevalent in tumors characterized by low copy number alterations
We identified multiple rare, but mutually exclusive alterations associated with loss NCor/SMRT - These alterations may predict lack of response to endocrine therapy
Thanks!
Chris Sander Niki Schultz Rileen Sinha Anders Jacobsen Boris Reva Xiaohong JingWei-Qing Wang
Chuck Perou Katie Hoadley
...and the whole TCGA Breast AWG!
Appendix(A
Luminal A Recurrently Mutated Genes (q < 0.05) data from TCGA, Ellis et al., Banerji et al
Her2-enriched
Basal-like
Luminal B
# of mutations per sampleLuminal A # of SigGenes ( q<0.05)
0 20 40 60 80
PIK3CA MAP3K1 GATA3 TP53 CDH1 MLL3 MAP2K4 NCOR1 AKT1 PTEN
RUNX1 CTCF CBFB SF3B1 MED23 WNT7A TBL1XR1 TBX3 GPS2 FOXA1
DGKG SMCHD1 KRAS CCND3 NKAIN4 HIST2H2BE HIST1H3B SHD GPR32
A)
8q.24AURKACDC25BCCNA2AURKB
CDK1CCNA1BIRC5 PLK1
AURKA
PLK1
CDC25B/C
Mitosis
CDK1Cyclin-A/B
C)
Copy Number HighHighLow
Diff
eren
tially
Exp
ress
ed G
enes
B)
TP53BP1POLH
POLI
MLH3POLK
0%
10%
20%
30%
40%
50%
60%
TP53
(mut) MYC
(amp) 20
q
(gain)
5q
(loss
)PIK
3CA
(mut)
Copy Number HighOtherp < 0.01p < 0.05
Luminal A
Luminal A Samples
**
*%Sa
mpl
es
*
**
**
****
Appendix(B
ER Positive Targets (BRCA_ER_POS)
0.0
0.8
Enric
hmen
t sco
re (E
S)
ClassA (positively correlated) ClassB (negatively correlated)
p < 10 , FDR = 0.03-3
CNH tumors are ER+
A)
8q.24AURKACDC25BCCNA2AURKB
CDK1CCNA1BIRC5 PLK1
AURKA
PLK1
CDC25B/C
Mitosis
CDK1Cyclin-A/B
C)
Copy Number HighHighLow
Diff
eren
tially
Exp
ress
ed G
enes
B)
TP53BP1POLH
POLI
MLH3POLK
0%
10%
20%
30%
40%
50%
60%
TP53
(mut) MYC
(amp) 20
q
(gain)
5q
(loss
)PIK
3CA
(mut)
Copy Number HighOtherp < 0.01p < 0.05
Luminal A
Luminal A Samples
**
*%Sa
mpl
es
*
**
**
****
Appendix(B
0%
10%
20%
30%
40%
50%
60%
70%
80%
TP53
(mut)
MYC
(amp) 20
q
(gain)
5q
(loss
)PIK
3CA
(mut)
%S
ampl
es
Copy Number High Other p < 0.01 p < 0.05
Luminal B
**
**
**
*
*
*
*
Luminal B have similar subgroup
Luminal B Samples
Diff
eren
tialy
Exp
ress
ed G
enes
Copy Number High
... E2F1 BCAT1 AURKA AURKB KIF2C CENPA CCNA2 CDCA5 CDCA3 TAF2 CDC20 CDC25B PLK1 ...
High
Low
ER Positive Targets (BRCA_ER_POS)
0.0
0.8
Enric
hmen
t sco
re (E
S)
ClassA (positively correlated) ClassB (negatively correlated)
p < 10 , FDR = 0.03-3
CNH tumors are ER+