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Next-Generation Sequencing is a Valuable
Tool in an Oncologist’s Practice -
ABSOLUTELY
Kimberly Blackwell MD
Professor of Medicine
Duke Cancer Institute
Miami Breast Meeting
March 8, 2014
Overview
Evolutionary Strategies Endocrine Therapy
HER2 Based Therapy
Next steps: Revolutionary? Identifying potential clinical trials
Next Generation Sequencing Trials\
Identifying Prognostic Mutations
Reason #1: Identifying Potential Trial
Candidates
HER2 mutation identified in HER2- breast cancer in
ACOSOG Z1031 by next generation
massively parallel sequencing
SURGERY
Postmenopausal • Clinical Stage II or III • ER+ (Allred 6-8) • HER2-
Exemestane
Letrozole
Anastrozole
R
BIOPSY
HER2 mutation Stage ER PR HER2 V777L IIB + + Negative
del.755-759 IIB + + Negative
25 Patients with HER2 Somatic
Mutations
• Each blue circle represents a patient.
• From 8 publications with a total of 1,499 patients.
• 20% of patients have mutations at amino acids 309 or 310.
• 68% of patients have mutations at amino acids 755-780.
Bose, R., et al., Cancer Discov, 2013. 3(2): p. 224-37.
A Phase II Trial of Neratinib in Metastatic
HER2 Non-amplified but HER2 Mutant Breast Cancer
CLIA Tumor HER2 Sequencing
HER2 Negative Metastatic Breast Cancer
*Neratinib 240 mg P.O. daily
days 1-28 each cycle #
** May continue neratinib at progression if trastuzumab is added in the most recent amendment
Continue therapy until
disease progression** or unacceptable toxicity
*Prophylactic loperamide
during 1st cycle. May
escalate to 320 mg in the
most recent amendment
# Each cycle is 28
days
HER2 Mutation
Negative
Not eligible for
study treatment
Screening Consent & Pre-registration
HER2 Mutation Positive
Consent to treatment & Registration
Tumor measurement every 2 cycles
Reason #2: Identifying Potential Compounds
that Have a Higher Likelihood of Benefitting
Patients (AKA the National Cancer Institute
thinks it is time!)
Treatment MBC according to genomic alterations SAFIR01
423 patients consented
CGH arrays: 287 patients
Biopsy of metastasis: 404 patients
194 targetable genomic
alterations 25%
treatment driven by
genomics in 48 patients
+ 4 patients ERBB2 amp CGH array
12%
Andre, F, et al. ASCO 2013
Therapies matched to the genomic alterations
Rapalogs
FGFR FGFR/VEGFR
EGFR/mTOR
AKT
TORC1/2
PI3K
16 regimens
CDK4 Raf
MET
MDM2
MGMT CHEK1
EGFR
FAK
Targets of the drugs
Efficacy data on 48 patients treated with therapy matched to genomic analysis
Efficacy n (%)
Objective response 4 (9%)
SD>16 weeks 8 (19%)
OR + SD>16 weeks 12 (28%)
Progression within 16 weeks 32 (72%)
Ongoing therapy SD <16 weeks 4
Erbb2 conversion (n=4) 1 OR
1 long term SD
(10 months)
Targets picked-up: EGFR amplification AKT gene alteration
FGF-amplified BC IGF1R amplification
12 out of 404 (3%) patients got some benefit from the biopsy procedure and genomic profiling
MATCH NCI Study
• Umbrella protocol multiple, single-arm phase II
• CTEP-IND for protocol template
• Initially focused on single-agents
– Combinations will be considered for targets that have validated combination targeted therapy
• Tumor biopsies & sequencing at progression to illuminate resistance mechanisms
• Screen 1500 to 3000 patients that progressed following standard therapy to enroll 500 – 1000
• Limit enrollment to 1000 eligible patients – Restrict ratio of common vs. uncommon histologies screened – Adjust screening ratio to achieve adequate representation of
rare tumors among those enrolled on treatment • 75% “common”: breast, NSCLC, colon, prostate, (lymphoma) • 25% “rare” tumors
SCHEMA
Study agent
Complete or partial
response (CR+PR)1
Actionable
mutation detected
No additional actionable mutations, or withdraw consent
Genetic sequencing
Progressive
disease (PD)1
Stable disease
(SD)1 for 6 months
Drug
holiday PD
Study agent
Off study
PD
Check for additional actionable mutations3,4
Stable disease or
better2
Continue on
study agent
until
progression
Continue on
study agent
until
progression
Course 1
Course 2
1CR, PR, SD, and PD as defined by RECIST
2Stable disease is assessed relative to tumor status at re-initiation of study agent 3
4Rebiopsy; if additional mutations, offer new targeted therapy
Reason #3: Defining Prognosis and
Potentially Actionable Mutations in Metastatic
Breast Cancer
Extraordinary Responders to lapatinib with trastuzumab
primary-refractory IBC share common cancer genotype
PIK3CA H1047R TP53 R273H
ERBB2 amplification TP53 E204
PIK3CA H1047R
ERBB2 amplification
TP53 Y205fs*3
CDKN2A loss
CDKN2B loss BRCA2 mutation
CDKN2A loss
CDKN2B loss PALB2 mutation
TBX3 splice
BLM R643H
PTEN C296fs*1
Patient 3 Patient 2 Patient 1
O’Shaughnessy, J. SABCS 2013
ERBB2 amplification
original core biopsy
4th patient with identical phenotype and genotype recently identified
Patients 1 and 2 with multple amplicons: FGFR1, MYST3, ZNF703, CDK6
All Rights Reserved, Duke Medicine 2011
ABC Metastatic TNBC Clinical Trial/ Tissue Procurement (Clinical Breast Cancer, 2013. 13:6, 416-20)
1. Metastatic
Biopsy
2. Germline DNA
3. Primary
Tumor Block
San Antonio Breast Cancer Symposium – Cancer Therapy and Research Center at UT
Health Science Center – December 10-14, 2013.
This presentation is the intellectual property of the author/presenter. Contact them at [email protected] for permission to reprint and/or distribute.
Total Population (38) Tissue Population (34)
Age 50 (30-76) 50 (30-76)
PFS (mo.) 9.2 (7.8-25.1) 14.6 (6.7-28.8)
OS (mo.) 21.6 21.9
All Rights Reserved, Duke Medicine 2011
Most Frequently Occurring Mutations
• 122 genes somatically mutated in >1 patient – Mean 10 mutations/sample (Range 0-42)
– 74 genes had mutations occurring ≥3 times.
San Antonio Breast Cancer Symposium – Cancer Therapy and Research Center at UT
Health Science Center – December 10-14, 2013.
This presentation is the intellectual property of the author/presenter. Contact them at [email protected] for permission to reprint and/or distribute.
1
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Identified as Potential Cancer Target
All Rights Reserved, Duke Medicine 2011
Genes With Mutations Associated with Progression Free Survival
Gene (# of Patients
Mutations)
Mutation (mo.) Wild Type (mo.) P-value
WNK1 (3) 1.4 7.3 0.03
TP53 (10) 4.7 8.2 0.04
JAK1 (3) 1.6 7.3 0.04
DCHS2 (5) 2.8 7.5 0.04
ATXN7 (3) 10.8 6.6 0.03
MST1 (3) 11.4 6.2 0.04
WNK1 TP53 JAK1 DCHS2
All Rights Reserved, Duke Medicine 2011
Genes with Mutations Associated with Disease Free Interval
Gene (# of
Mutations)
Mutation
(mo.)
No Mutation
(mo.)
P-value
HGF (3) 107.4 19.4 0.009
PLXNA3 (4) 37.9 26.0 0.02
CSDE1 (3) 39.6 25.4 0.02
ZNF710 (4) 86.2 19.3 0.03
CNN2 (3) 103.9 22.3 0.03
PAPLN (3) 53.8 23.6 0.03
SETBP1 (2) 81.2 24.0 0.04
MTOR (4) 59.3 22.8 0.05
This presentation is the intellectual property of the author/presenter. Contact them at [email protected] for permission to reprint and/or distribute.
All Rights Reserved, Duke Medicine 2011
Genes with Mutations Associated with Overall Survival
Gene (# of
Mutations)
Mutation (mo.) Wild Type (mo.) P-value
TP53 (10) 17.5 25.9 0.02
ITSN2 (3) 7.6 27.6 0.03
ALDH8A1 (2) 6.5 27.1 0.05
SPHKAP (2) 66.6 23.5 0.03
TP53 ITSN2 ALDH8A1 SPHKAP
This presentation is the intellectual property of the author/presenter. Contact them at [email protected] for permission to reprint and/or distribute.
All Rights Reserved, Duke Medicine 2011
Actionable Mutations
• Studied in Breast Cancer
– p53: Vaccine, Gene therapy, Wee-1 inhibitors, Kevetrin
– PARP: PARP Inhibitors
– ESR (ER) : Alternative Endocrine Therapies
– JAK1: JAK1 Inhibitors
– mTOR: mTOR Inhibitors
• Not Studied in Breast Cancer (yet)
– Dynein: hsp90 Inhibitors, HDAC inhibitors
– MST1: Anti-MST1 receptor (Ron) antibodies
– ROS-1: Inhibitors
– HGF: Antibodies against c-met; Inhibitors against c-met
– ALDH8A1: Disulfiram
Source: www.clinicaltrials.gov
This presentation is the intellectual property of the author/presenter. Contact them at [email protected] for permission to reprint and/or distribute.
There has been a revolution of Science but the
clinical application has lagged behind….next-gen
sequencing will catch the science up!
Where the Generator is
Busted:
Bcr-Abl CML (4,500)
C-KIT mutation (1,000)
EGFR Mutation (1-2,000
patients)
HER2 Driven Breast
Cancer (40,000 patients)
Everything Else Where
Several Sockets are
Busted (191 CAN-
genes): 1.4 Million
patients
Hanahan and Weinburg, Cell, 2000
Wood LD, et al. Science, 2007.
WNT
Cell
ECM
Growth factors (e.g. HRG, EGF, TGF a )
Nuclear receptors (e.g. estrogen)
Survival factors (e.g. IGF1)
Cytokines (e.g. ILs , IFNs )
Death factors
(e.g. FasL )
Anti - growth factors (e.g. TGF b )
GPCR ligands
Frizzled Dishevelled
GSK - 3 b
APC
Tubulin
TCF
Integrins
b - Catenin b - Catenin:TCF E - Cadherin CdC42 PI3K Rac
Fak Cas Crk Src
Fyn Shc
NF1
Ras RTK Grb2 SOS Ral MEK MAPK MAPK
MEKK
PLC
PKC Mos MKKs JNKs
ELK
Myc:Max
Max:Max Fos
JUN
Abl
7 - TMR
CdC42 Rac Rho
G - Prol Ad Cycl PKA CREB
PKC NF k B
NHR (e.g. ER)
NF k B
P13K Akt Akka IKB
PTEN ?
Stat 3.5
Stat 3.5
Stat 3.5
Bcl XL
Caspase 9
Cytochrome C
Jaks
Bad Bid Mitochondria
Bim , etc. Abnormal sensor
Bcl - 2
Cell Death (Apoptosis) Caspase 8
Fap
FADD Bcl - 2
Bax
ARF
p53
Mitochondria
MDM2
DNA damage sensor Cell
Proliferation (cell cycle)
Changes in Gene
Expression
Cycl E:CDK2 p21
p27
E2Fs
Rb
p16
Cycl D:CDK+ p15 Smads
RTK
Cytokine R
Decoy R
Fas
Surface Ag
TGF b R
HPVE7
IAP
Don’t be an Evolutionist, Be a
Revolutionist when taking care of
your breast cancer patients!
THANKS