Intergenic Fusions in Advanced HR+ Breast Cancer

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1 Intergenic Fusions in Advanced HR+ Breast Cancer Leif W. Ellisen, MD, PhD Program Director, Breast Medical Oncology

2 Disclosures: Lief W. Ellisen, MD, PhD, has disclosed no relevant financial relationships. 2

3 Case Presentation CRO10 56yo F presented with T2N0 primary ER/PR+, HER2- IDC Received adjuvant AC chemotherapy followed by tamoxifen Presented 24 months post chemo with bone/liver metastases No response to first-line treatment with exemestane Further progression shortly after first-line chemotherapy (capecitabine) Expired <4 years post initial diagnosis Snapshot mutation testing of both primary tumor and metastatic lesion: No identifiable mutation 3

4 Primary breast cancers exhibit moderate mutation burden 4 Vogelstein et al. Science 339:6127 (2013)

5 Significantly mutated genes and correlations with genomic and clinical features 5 Koboldt et al, Nature 490:7418 (2012)

6 Proportion of cases with mutated driver genes 6 Nik-Zainal et al, Nature 534:7605 (2016)

7 Transcriptome and data-mining analysis reveals intergenic fusions in solid tumors 7 Stransky et al, Nature communications 4846 (2014)

8 Employing Anchored Multiplex PCR assay to detect expressed gene fusions in ER+ breast cancer Employs ng amounts of TNA from FFPE Primarily sequences cdna Agnostic as to fusion partner Assesses gene expression Current platform interrogates >60 genes. 8 Zheng et al. Nature medicine 20:12 (2014)

9 9 Expressed fusions identified in primary and metastates of ER+ advanced breast cancer patients

10 Expressed fusions identified in 14% (24/173) of ER+ metastatic breast cancer patients Different Chromosome (11; 46%) Same Chromosome-Different Orientation (6; 25%) Same Chromosome-Same Orientation (7; 29%) 10

11 ESR1 is the most common fusion partner gene (40% of identified fusions) ESR1 AF1 DBD HINGE LBD PLEKGH1-ESR1 RhoGEF PH AF1 DBD HINGE LBD TNS3-ESR1 C1 C2 AF1 DBD HINGE LBD ESR1- CoA5 AF1 DBD ESR1-CCDC170 AF1 SMC Prok B ATPase 11

12 12 Oncogenic kinases and ESR1 comprise the majority of detected fusions

13 FISH analysis confirms gene-specific rearrangements Patient CRO10: CTNNBL1/RAF1 fusion RAF1 13 Maristela Onozato

14 FISH analysis in primary and metastatic lesions concurs with AMP assay ESR1/COA5 fusion ESR1 14 Maristela Onozato

15 Gene amplification and rearrangement revealed by FISH analysis RPS6KC1/AKT3 fusion AKT3 15 Maristela Onozato

16 16 Protein expression of multiple AKT3 fusions

17 17 Fusions are uncommon in primary ER+ breast cancers (N=300)

18 18 In-frame fusions encode novel, potentially deregulated oncogenic kinases

19 Kinase fusions produce stable proteins and activate PI3 Kinase/mTOR pathway MCF10A 19 Sheng Sun

20 Novel kinase fusions promote oncogenic phenotypes in 3D mammary epithelial cultures MCF10A β-catenin DAPI Merged 50μm 20 Karina Matissek

21 Kinase fusions alter hormone dependence and response in cell based HR+ breast cancer models MCF-7 Trametinib (MEKi) 100 % Viable Cells Vector CTNNBL1-RAF1 *** 21

22 Kinase fusions alter hormone dependence and response to hormonal therapy in cell based HR+ breast cancer models MCF-7 ** * 22

23 Activation of cyclin D and hormone-independent proliferation by AKT3 fusion is comparable to oncogenic AKT E17K MCF7 PIK3CA Corrected Cells Estrogen Withdrawal Activated AKT stabilized Cyclin D1 PI3K AKT p GSK3β p Cyclin D1 S9 Inactivation T286 FOXO4-mediated proteasomal degradation 23

24 RPS6KC1/AKT3 is a constitutively membrane associated and active kinase

25 AKT3 fusion contributes to tumor progression in vivo + E2 Vector S6KC1- AKT3 or AKT1 E17K Fold change in tumor size * ** Days 25

26 AKT3 fusion contributes to hormone independence in vivo Vector - E2 + E2 S6KC1- AKT3 - E2 + Palbociclib E2 Withdrawal E2 Withdrawal + Palbociclib * Vector S6KC1-AKT3 Vector S6KC1-AKT3 26

27 Demographics and clinical presentation are similar for fusion positive vs. negative patients 27 Characteristic Fusion (+) Fusion (-) Age at diagnosis, years Median Range Stage at Diagnosis: I 10% (1/10) 20% (10/53) II 50% (5/10) 58% (29/53) III 30% (3/10) 22% (11/53) IV 10% (1/10) 0% (0/53) ER 80% (8/10) 98.1% (52/53) PR 90% (9/10) 92.4% (49/53) Adjuvant Tamoxifen (%) 90% (9/10) 71.7% (38/53) Adjuvant AI (%) 40% (4/10) 32% (17/53) Any Adjuvant Hormonal Therapy 90% (9/10) 92.3% (49/53) Adjuvant Chemotherapy (%) 70% (7/10) 55.7% (29/52) Characteristic Fusion (+) Fusion (-) Age at diagnosis, years Median Range Stage at Diagnosis: I 14.3% (2/14) 15.6% (15/96) II 42.9% (6/14) 45.8% (44/96) III 21.4% (3/14) 13.5% (13/96) IV 21.4% (3/14) 21.9%(21/96) ER + (%) 100% (14/14) 93.8% (90/96) PR + (%) 71.4% (10/14) 72.9% (70/96) Adjuvant Tamoxifen (%) 28.6% (4/14) 56.3% (54/96) Adjuvant AI (%) 71.4% (10/14) 44.8% (43/96) Any Adjuvant Hormonal Therapy 92.9% (13/14) 86.5% (83/96) Adjuvant Chemotherapy (%) 71.4% (10/14) 57.3% (55/96) Matched Primary/ Metastasis Cohort Clinical Genotyping Cohort

28 Fusions predict poor outcome in ER+ breast cancer patients Survival Post Metastasis Survival Post Metastasis Survival Probability Fusion - Fusion + p = 0.01 Survival Probability Mutation - Mutation + p = Years since Metastasis Years since Metastasis 28

29 Fusions predict poor outcome in ER+ breast cancer patients Overall survival Overall survival Survival Probability Fusion - Fusion + Survival Probability Mutation - Mutation + p = p = Years since Diagnosis Years since Diagnosis 29

30 Summary and Conclusions Fusions appear prevalent in advanced ER+ breast cancer Commonly involve oncogenic kinases and ESR1 Can confer aggressive behavior and hormone independence Associated with shortened overall survival Potentially Actionable Support routine testing in patients with advanced disease. 30

31 Acknowledgements Ellisen Lab Sheng Sun Kristofer Patel Mihriban Karaayvaz Vinod Saladi Shuxi Qiao Siang Boon Koh Aiko Nagayama Varunika Vivekanandan Nicole Smith Former Lab Karina Matissek Andrew Schultz MGH Pathology Maristela Onozato Jesse Lee John Iafrate Dennis Sgroi Avon International Investigators Jessica St. Louis Paul Goss Funding NIH: NCI; NIDCR DOD Avon Foundation MGH ECOR Scholars Komen Foundation Terri Brodeur Foundation National Cancer Center 31