The Molecular Diversity of Luminal A Breast Tumors · The molecular diversity of Luminal A breast tumors ... Luminal B PAM50: ... N-Cor NCOR1 5% 2% TBL1XR1 2% GPS2 3% ANKRD11

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'

Her2-negative


ER-positive

ER - negative'PAM50: Basal'

PAM50: Luminal B'

PAM50: Luminal A'



Breast Cancer'

Her2-negative


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





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





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)


CDK1CCNA1BIRC5 PLK1

AURKA

PLK1

CDC25B/C

Mitosis

CDK1Cyclin-A/B

C)


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)


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


MA

P3K

18p

11


Chromosomes

Sam

ples


utat

ions


Mutation Type

MAP3K1 mutations

A)

B)

0

5

10

15

20

25


5

10


#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



C)

D)

E)

Samples

Mutated genes

CN

A





Somatic mutations

PIK3CA

GATA3

AKT1

MAP3K1

TP53


MA

P3K

18p

11


Chromosomes

Sam

ples


utat

ions


Mutation Type

MAP3K1 mutations

A)

B)

0

5

10

15

20

25


5

10


#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



C)

D)

E)

Samples

Mutated genes

CN

A





Which pathways are most de-regulated?

30.5%

8% 8.5%Gene CGene B

Gene D

Gene A54%

t

●

●

●●

●

●●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●●

●

●

●●●

●

●

●

●

●

●

●

●

●

●

●●

●

●

●

●

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


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


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


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


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)


CDK1CCNA1BIRC5 PLK1

AURKA

PLK1

CDC25B/C

Mitosis

CDK1Cyclin-A/B

C)


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)


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)


CDK1CCNA1BIRC5 PLK1

AURKA

PLK1

CDC25B/C

Mitosis

CDK1Cyclin-A/B

C)


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)


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+

Documents

The Molecular Diversity of Luminal A Breast Tumors · The molecular diversity of Luminal A breast tumors ... Luminal B PAM50: ... N-Cor NCOR1 5% 2% TBL1XR1 2% GPS2 3% ANKRD11