Kinome Profiling: The Potential in ER-Negative Patients. Charles M. Perou, Ph.D. Departments of Genetics and Pathology

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1 Kinome Profiling: The Potential in ER-Negative Patients Charles M. Perou, Ph.D. Departments of Genetics and Pathology Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill, North Carolina, USA

2 HER2 CRYAB c-kit EGFR/HER1 Keratin 5 Keratin 14 Keratin 17 P-Cadherin Basal-like subtype % of tumors 2. 75% of TNBC 3. >85% TP53 mutant 4. BRCA1 associated 5. RB pathway mutant 6. HER1-RAS-MEK pathway ~50% are HER1 by IHC+ (Nielsen et al., CCR 2004) Luminal Proliferation HER1 IHC

3 TBCRC001: Randomized Phase II study of Cetuximab in Combination with Carboplatin in Stage IV Triple-Negative Breast Cancer. Carey et al., JCO 2012 Metastatic TNBC Cetuximab vs. Cetuximab + Carboplatin

4 = above average = average = below average Statistically associated with Basal-like and with the high expression of HER1 profiles EGFR associated expression profiles vary with breast tumor subtype, Hoadley et al., BMC Genomics Jul 31;8(1):258 (2007)

5 Basal-like Breast Cancer Results from TCGA et al., Nature % Amplified 0 mutants 48% Amplified, 9% mutant 32% Amplified, 1 G12V mutant INPP4B 28% deleted 1 mutant 31% Amplified 1 mutant (not V600E) 50% High expression Moyano et al., 2006 MEK1-pathway total = ~80% with some possible pathway activating event 31% deleted 1 mutant 68% amplified 1 mutant PIK3CA-pathway total = ~90% with some possible pathway activating event

6 Basal-like Breast Cancer Results from TCGA et al., Nature 2012 INPP4B MEK inhibitors AZD6244 GSK GDC-0973 MEK1-pathway total = ~80% with some possible pathway activating event PIK3CA-pathway total = ~90% with some possible pathway activating event

7 Cell, Apr 13;149(2):307-21, 2012 (PMID: ) Gary Johnson, PhD, Chair, Department of Pharmacology, University of North Carolina

8 Multiplexed Inhibitor Beads (MIBs) MIBs consist of multiple immobilized kinase inhibitors layered into an affinity column based on an inhibitor specificity gradient (specific nonspecific) MIB-MS, couples inhibitor beads with quantitative Mass Spectrometry to determine protein kinase amounts and behavior 5 mg of protein / bead

9 Monitoring Kinome Activity with MIB-MS Binding of kinases to MIBs is a function of both affinity and activation state of the kinases + Lapatinib Provides a tool to interrogate the Kinome, which is all expressed kinases of a cell or tissue inhibited Activated

10 RAF/MEK/ERK pathway is a target in TNBC and Basal-like more in tumor more in tumor Duncan et al., Cell 2012

11 MIB-MS Profile in response to MEK inhibition in a human TNBC cell line (SUM159) SUM159 cells + AZD6244 RAF1 ERK1 AXL DDR1 PDGFRb Duncan et al., Cell 2012

12 PDGFRb Inhibition Synergizes with AZD6244 to induced Growth Arrest Sorafenib FDA approved ERK inhibited Duncan et al., Cell 2012

13 MEK inhibitor reprogramming is observed in the C3-Tag Mouse Model of TNBC Duncan et al., Cell 2012 Herschkowitz et al., GB 2007

14 Combination of AZD6244 and Sorafenib Causes Tumor Regression in C3-Tag TNBC Mouse Model ERK inhibited * p-value 0.007

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16 Dynamic reprogramming of the kinome in response to targeted MEK inhibition in Triple-Negative Breast Cancer. Duncan et al., Cell, Apr 13;149(2): (2012) PDGFRb PDGFRb

17 Dynamic reprogramming of the kinome in response to targeted MEK inhibition in Triple-Negative Breast Cancer. Duncan et al., Cell, Apr 13;149(2): (2012) PDGFRb PDGFRb PDGFRb

18 Basal-like Breast Cancer Results from TCGA et al., Nature 2012 PIK3CA inhibitors PIK3CA + mtor inhibitors MEK inhibitors mtor inhibitors MEK1-pathway total = ~80% with some possible pathway activating event PIK3CA-pathway total = ~90% with some possible pathway activating event

19 Combined PI3K/mTOR and MEK Inhibition Provides Broad Anti-Tumor Activity in Faithful Murine Cancer Models. Roberts, Usary, Darr et al., CCR, 2012 TP53-/- tumor (T11) Claudin-low mouse mammary tumor C3-Tag Basal-like mouse mammary tumor

20 Kinome Reprogramming Summary 1. The protein kinome (i.e. all expressed kinases of a cell) forms a dynamic and interconnected network 2. Some tumor types are highly dependent upon a single mutant kinase, and a single drug can elicit a dramatic response (EGFR-lung, EML4/ALK-lung, BRAF-melanoma, others) 3. For many tumor types, mutant kinases are not present, but wild type kinases are present and still represent critical signal transduction components 4. For many tumor types possibly including breast, combinations of kinase inhibitors may be needed. However, novel combinations likely have toxic side effects, and thus, great care is needed as we test these new regimens