Squamous Cell Carcinomas: Genomic Discovery and...

2/19/13

1

Squamous Cell Carcinomas: Genomic Discovery and Biomarkers

Peter Hammerman MD, PhDDana Farber Cancer Institute

Treatment of Advanced NSCLCAdenocarcinoma Squamous Cell

No Tumor GenotypingChemotherapy

Targeted agents largely ineffective to date

Tumor GenotypingPersonalized Therapy

KRASUnknown

g g g y

EGFR

ALKB

RA

F

PIK

3CA

ER

BB

2

RO

S1

RET

AK

T1

MA

P2K

1

2/19/13

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2012—Year of retrospective NGS studies of lung cancer

A second screen–SNP array analysis demonstrates amplification of FGFR1 in 6% of NSCLC (45/733):3% of adenocarcinomas and 20% of squamous carcinomas

WHSC1L1

FGFR1

FLJ43582

Weiss et al and Dutt et al

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3

FGFR1 amplification predicts sensitivity to FGFR kinase inhibitors in some cell lines

Phase I of BGJ398 presented at AACRResponses in FGFR1 amplified lung SqCC, one >6 mos

MYCLMCL1

RELNFE2L2

SOX2PDGFRA

TCGA LUSC Amplifications

PDGFRA

EGFRFGFR1

CCND1CCND1

CRKL

ERBB2

MDM2

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FGFR2/3 Mutations in Lung SqCC

FGFR-driven transformation is blocked by multiple FGFR kinase inhibitors

BGJ398 Ponatinib

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Ba/F3 Cell Profiling of FGFR2 mutations reveals sensitivity to a panel of inhibitors

100W290Cb

W290Cc

S320Cb

K660Ebon

100 W290Cb

W290Cc

S320Cb

n

-3 -2 -1 0 10

50

K660Eb

K660Ec

K660Nb

K660Nc

WT2b

EGFR insNPG

Ba/F3 +IL3

Log uM BGJ398

Gro

wth

inh

ibiti

o

-3 -2 -1 0 10

50

K660Eb

K660Ec

K660Nb

K660Nc

WT2b

EGFR insNPG

Ba/F3 +IL3

Log uM AZD4547

Gro

wth

inh

ibiti

on

Response to pazopanib in a patient with a FGFR2 mutation

FGFR2 P253R

2 weeks pazopanib

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Revisiting the kinome by exome sequencing

Radiographic response of a patient with a S768R DDR2 mutation treated with dasatinib plus erlotinib.

2/19/13

7

40

60

80

100

13

2

atio

ns/M

b

Syn.Non syn

Syn.MissenseSplice siteNonsense

Frame shiftIn frame indelOther non syn.

Significantly Mutated Genes in Lung Sqcc

7%

8%

15%

3%

20%

12%

16%

8%

15%

81%551 551

70 50 30 10# individuals with mutation

0.5 2.0 3.5

RB1

NOTCH1

NFE2L2

HLA-A

MLL2

KEAP1

PIK3CA

PTEN

CDKN2A

TP53

-log10(q-value)

0

20

40

# m

utaNon syn. Nonsense

g (q )

NFE2L2/KEAP1/CUL3 Mutations in KEAP1 are lof (frequent LOH of second allele)

Mutations in NRF2 cluster in DLG and ETGE motif -> prevent KEAP1 interaction -> results in NRF2 stabilization and nuclear entry

Shibata et al. PNAS 2008

In head and neck cancer mutations in NFE2L2/KEAP1/CUL3 are mutually exclusive with HPV+ (p<0.02); TP53 (p=0), CDKN2A (p<0.001)

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500 1000 2000 cells 500 1000 2000 cells

A549 H460

2 KEAP1 mutant lung cancer lines are sensitive to siRNA targeting NFE2L2

A549 H460

siNTC

siNRF2

siNTC

siNRF2

GAPDH

siNTC-D3

siNRF2-D3

siNTC-D7

siNRF2-D7

siNTC-D3

siNRF2-D3

siNTC-D7

siNRF2-D7

NRF2

Mohamed Abazeed

NRF2 Mutant SCC Line

1000 2000 4000 #cells

LK2

siNTC

siNRF2

120 00

NRF2 gene exp. with siNRF2 KD in LK2 cells

120 00

NQO1 gene exp. with siNRF2 KD in LK2 cells

NRF2

GAPDH

siNTC-D6

siNRF2-D6

100.0

6.2

0.00

20.00

40.00

60.00

80.00

100.00

120.00

siNTC-D6 siNRF2-D6

Rel

ativ

e E

xpre

ssio

n

100.0

13.2

0.00

20.00

40.00

60.00

80.00

100.00

120.00

siNTC-D6 siNRF2-D6

Rel

ativ

e E

xpre

ssio

n

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Radiosensitization with PI3K antagonism

Lung Squamous

Immunotherapeutic Biomarkers

Head and neck Squamous

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Summary—Lung Sqamous Cell Cancer

• Most altered RTK pathway in lung SqCC is FGFRFGFRs

• Most altered kinase pathway is PI3K• Role for PI3K antagonists in personalized

radiotherapyLikely will be a role for personalized• Likely will be a role for personalized immunotherapy

• Genotype interactions in many dimensions should inform therapeutic decision making