Download 2015 UCSF Breast Oncology Program Scientific Retreat California

2015 UCSF Breast Oncology Program Scientific Retreat
California Breast Cancer Research Program Poster Session
Table of Contents
Poster Category
Detection and Biomarkers Poster
Epidemiology and Population Science Poster
Molecular Biology Poster
Physical Science Poster
Therapeutics and Clinical Trials Poster
Page
2-15
16-18
19-30
31-36
37-45
The Breast Oncology Program Scientific Retreat retreat is supported in part by:
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Nektar Therapeutics
California Breast Cancer Research Program (21MB-0004)
Celgene Corporation
Puma Biotechnology
UCSF Helen Diller Family Comprehensive Cancer Center Support Grant (P30 CA082103)
(1)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #1
Targeted viral capsids as imaging agents for breast cancer detection
Ioana L. Aanei1, Adel M. ElSohly1, Chawita Netirojjanakul1, Michelle E. Farkas1, Matthew B.Francis1,
Joe W. Gray2
Author Affiliations:
1 UC Berkeley Dept. of Chemistry
2 Oregon Health and Science University
Presenting Author:
Ioana Aanei
UC Berkeley Dept. of Chemistry
Matthew Francis Group
[email protected]
Abstract
Recent advances in the field of cancer nanotechnology have allowed for the development of promising
platforms for medical diagnostics and therapeutics. Compared to other nanoparticles available and in
use today, the potential of protein-based nanoscale carriers has been relatively unexplored. The work
herein describes a robust and modular platform for antibody-based targeting and delivery through the
preparation of genome-free bacteriophage MS2 viral capsid-antibody conjugates. These bioconjugates
provide an all-protein nanoparticle system with distinguishable interior and exterior surfaces that are
amenable to facile diversification for use in a variety of imaging modalities, including PET, MRI and
fluorescence. The in vitro and in vivo properties of agents targeted against HER2 and EGFR receptors
overexpressed on several breast cancer models were evaluated. In vitro studies confirmed that the
binding affinity and specificity of the antibody are not affected by conjugation to the viral capsid. Livecell confocal microscopy studies confirmed the interaction with the targeted receptors and indicated
rapid internalization of the agents, followed by their localization to intracellular vesicles. PET imaging
and subsequent biodistribution studies performed in orthotopic and subcutaneous xenograft murine
tumor models demonstrated significant amounts of agents still present in the system 24 h postinjection, in contrast to reports using other viral capsids of similar size. Current efforts are aimed at
determining the sub-tumor localization of targeted versus untargeted agents. Future work will focus on
attaching therapeutic molecules through cleavable linkages to the interior surface of the protein shell for
drug delivery purposes.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(2)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #2
Detection of cerebrospinal fluid tumor cells and its clinical relevance in leptomeningeal
metastasis of breast cancer
Jin Sun Lee, Michelle Melisko, Mark Jesus M. Magbanua, Andrea Kablanian, Janet H. Scott, and John
W. Park
Author Affiliation:
Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of
California San Francisco, CA 94115, USA
Presenting Author:
Jin Sun Bitar
hematology/oncology
[email protected]
Abstract
Purpose: We tested the feasibility of tumor cell detection in the cerebrospinal fluid (CSF) and studied its
clinical relevance in leptomeningeal metastasis (LM) of breast cancer.
Methods: CSF samples were collected from 38 metastatic breast cancer patients known or suspected
to have LM. Control CSF samples were collected from 14 individuals without solid tumor malignancy.
We used a modified CellSearch™ assay and an alternative EPCAM-based method involving
immunomagnetic enrichment followed by flow cytometry (IE/FC) to detect and enumerate CSF tumor
cells (CSFTCs). CSFTC were assayed at time of LM diagnosis and compared to standard
clinicopathologic factors. In addition, we assayed serial CSF samples over the course of LM-directed
therapy.
Results: We analyzed a total of 102 CSF samples with modified CellSearch. The CSFTC counts were
strongly correlated with the corresponding IE/FC results (Pearson’s r= 0.94). Twenty-eight out of 30
samples in which malignant cells were identified by CSF cytology were CSFTC-positive by modified
CellSearch. The baseline CSF samples from 21 patients eventually diagnosed with LM demonstrated
significantly higher numbers of CSFTCs than the control group (p=0.0202). There was no difference in
baseline CSFTC numbers between the 13 patients deemed not to have LM and the control group. In
patients with serial samples, it was possible to monitor CSFTC levels as a potential biomarker of LM
treatment response.
Conclusion: CSFTC detection using a modified CellSearch assay demonstrated high sensitivity in
detecting malignant cells in CSF and may be a promising method for diagnosing LM and measuring
changes in tumor cell counts during treatment to aid in response assessment and prognosis.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(3)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #3
Serial expression analysis of breast tumors during neoadjuvant chemotherapy reveals changes
in cell cycle and immune pathways associated with recurrence and response
Mark Jesus M. Magbanua1,2*, Denise M. Wolf1,3*, Christina Yau1,4,5*, Sarah E. Davis1,4, Julia Crothers1,2,
Alfred Au1,4, Christopher M. Haqq1,2,6, I-SPY 1 TRIAL Investigators, Laura Esserman1,4, John W. Park1,2,
and Laura van ’t Veer1,3
*
These authors contributed equally to this work.
Author Affiliations:
1 Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, CA USA
2 Division of Hematology/Oncology, University of California San Francisco, CA USA
3 Department of Laboratory Medicine, University of California San Francisco, CA USA
4 Department of Surgery, University of California San Francisco, CA USA
5 Buck Institute for Research on Aging, Novato, CA USA
6 Department of Urology, University of California San Francisco, CA USA
Presenting Author:
Mark Jesus Magbanua
Hem/Onc
[email protected]
Abstract
Background: The molecular biology involving neoadjuvant chemotherapy (NAC) response is poorly
understood. To elucidate the impact of NAC on breast cancer transcriptome and its association with
clinical outcome, we analyzed gene expression data from serial tumor samples of breast cancer
patients who received NAC in the I-SPY 1 TRIAL.
Experimental Design: Expression data were collected before treatment (T1), 24-96 hours after initiation
of chemotherapy (T2) and at surgery (TS). Expression between T1vsT2 (N=36) and T1vsTS (N=39)
were compared. Subtype was assigned using PAM50. Differences in early gene expression changes
(T2-T1) between responders and non-responders as defined by residual cancer burden (RCB) were
evaluated. Cox proportional hazards modeling was used to identify genes in residual tumors associated
with recurrence-free survival (RFS). Pathway analysis was performed with Ingenuity® software.
Results: Comparing expression profiles at T1vsT2 and T1vsTS detected significantly altered expression
of 150 and 59 transcripts, respectively. We observed notable down-regulation of proliferation and
immune-related genes at T2. Lower concordance in subtype assignment was observed between
T1vsTS (62%) as compared to T1vsT2 (75%). Analysis of early gene expression changes (T2-T1)
revealed that decreased expression of cell cycle inhibitors was associated with poor response.
Increased interferon signaling (TS-T1) and high expression of cell proliferation genes in residual tumors
(TS) were associated with reduced RFS.
Conclusions: Serial gene expression analysis revealed candidate immune and proliferation pathways
associated with response and recurrence. Larger studies incorporating the approach described here
are warranted to identify predictive and prognostic biomarkers in the NAC setting for specific targeted
therapies.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(4)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #4
Microfluidic filter-based detection and cytomorphological characterization of circulating rare
cell populations in blood of metastatic cancer patients.
Marc Jabon1, Mark Jesus M. Magbanua1, Jin Sun Lee1, Michael Pugia2, Karen Marfurt2, Julia Philips2,
Sunil Pandit2, Harwinder Sidhu2, Arejas Uzgiris2, and John W. Park1
Author affiliations:
1 Hematology/Oncology, University of California San Francisco, San Francisco, CA 94115
2 Siemens Healthcare Diagnostics, Elkhart, IN 46516
Presenting Author:
Marc Jabon
Department of Medicine, Division of Hematology & Oncology
Park Lab
[email protected]
Abstract
Background: The detection of circulating epithelial cells and other non-hematologic rare cells in the
blood offers an accessible source for characterization of metastatic disease. In this study, we tested the
performance of a microfluidic filter-based device for enumeration of rare cell populations in the blood of
cancer patients.
Methods: Whole blood samples from metastatic breast (n=19) and lung (n=21) cancer patients were
filtered through a porous membrane on a specially designed microfluidic slide. Smaller cells (<8μM),
such as blood cells, were allowed to pass through while larger cells, such as tumor cells, were collected
on the membrane. The cells on the membrane were then subjected to immunostaining for identification
using the following markers: cytokeratins (epithelial cells), CD45 (white blood cells), vimentin
(mesenchymal cells), CD144 (endothelial cells), PIWIL2 (putative breast cancer stem cells), TPBG/5T4
(putative lung cancer stem cells). Stained cells were enumerated via microscopic analysis. Circulating
epithelial cell counts were compared with circulating tumor cell counts enumerated via the CellSearch®
system.
Results: Preclinical testing using spiked cancer cells into healthy blood revealed a 90% recovery rate
with high reproducibility. The average counts (cells per mL of blood) for epithelial, endothelial,
mesenchymal/epithelial, and putative cancer stem cells were 0.40, 2.58, 0.68, and 0.15, respectively, in
breast cancer patients and 0.05, 4.54, 2.41, and 0.16, respectively, in lung cancer patients.
Interestingly, we found high numbers of nucleated cells (breast: 21.74, lung: 28.65) of unknown
significance that were negative for all the markers tested. Circulating rare cells enumerated in samples
collected from the same patient over the course of therapy demonstrated the feasibility of serial
analysis. Enumeration performed on duplicate blood samples using CellSearch® and our method
revealed a fair correlation (R²=0.46).
Conclusions: We demonstrate the feasibility of detection and characterization of circulating rare cells in
blood of metastatic patients using a novel microfluidic filter-based device. This antigen-independent
approach may eliminate potential bias when relying on cellular markers for enrichment of circulating
rare cells. However, the possibility of false-positive identification underscores the need for further
genetic analysis to provide proof of malignant origin and subsequent demonstration of clinical
relevance.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(5)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #5
Development of recombinant antibodies against recombinant EPO and not human EPO by
phage display technology
Lara Cobler1, Jose Antonio Pascual2, Peter Kristense3
Author affiliations:
1 HDFCCC
2 IMIM-Hospital del Mar (Barcelona, Spain)
3 Aarhus university (Aarhus, Denmark)
Presenting Author:
Lara Cobler
HDFCCC
Timmerman laboratory
[email protected]
Abstract
The aim of the project is to find an antibody specific for recombinant erythropoietin (rEPO), which could
be used for its detection in urine of athletes, using phage display. The central element of the project is
the fact that N-glycolyl-neuraminic (Neu5Gc) is a type of sialic acid which is not produced by human
beings but is present in the glycans displayed by recombinant EPO produced in non-human cells.
A single round selection from Predator library was performed to isolate recombinant antibodies that
bind to NeuGc. Then, alanine scanning was performed with a candidate antibody to find the valuable
amino acids for antigen binding. And, finally, random mutagenesis was performed in order to obtain an
antibody that recognizes Neu5Gc and not Neu5Ac (present in human EPO).
The resulting antibody was tested by ELISA, and clearly preferentially binds to rEPO and not to
recombinant EPO produced in human cells.
The present work describes an effective method to develop recombinant antibodies capable of
distinguish between very similar antigens.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(6)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #6
Characterizing the Tumor Immune MicroEnvironment (TIME) in high-risk ductal carcinoma in
situ
Tess O'Meara1, Michael J. Campbell1, Rita Mukhtar1, Ekene Obi-Okoye1, Booyeon Han1, Vick Tandon1,
Sarah Zheng1, Zelos Zhu1, Max Endicott1, Max Wicha2, Linda Lindstrom1, Gregor Krings1, Alfred Au1,
Frederick Baehner1, Joe Gray3, Laura Esserman1
Author affiliations:
1 University of California, San Francisco, CA
2 University of Michigan, Ann Arbor, MI
3 Oregon Health & Science University, Portland, OR
Presenting Author:
Tess O'Meara
UCSF Breast Surgery
Michael Campbell, PhD
tess.o'[email protected]
Abstract
Background: While some DCIS are likely not cancer, some have more risk than is realized. The
question remains: are there features that distinguish high risk DCIS lesions? The key may be to look
more closely at their underlying biology. DCIS features associated with high recurrence include large
size (>5cm), comedo necrosis, high grade, palpable mass, hormone receptor (HR) negativity, and HER2
positivity. Given that high grade, HR-neg invasive breast cancers have an inflammatory component
(significant macrophage infiltration) we sought to characterize the immune microenvironment of DCIS to
assess patterns of immune cell infiltrates associated with high risk DCIS lesions.
Methods: 53 cases of high grade DCIS, enriched for large lesions and history of recurrence were age
matched with 65 cases of non-high grade DCIS. Immunohistochemical analyses were performed as
single color stains for the following antigens: CD115, FoxP3, ALDH, Ki-67, HER2. Two color IHC was
performed for the following antigen pairs: CD68/PCNA; CD68/Mac 387; CD8/HLA-DR; CD68/MRC1,
CD24/CD44, and CD4/CD20. Stromal TILs were visually estimated as a percentage of total stroma per
section. HR status was determined from ER and PR staining results in pathology reports. For each case,
3 hot spots were identified and marked on 10 consecutive sections. Nuance multispectral imaging
software was used to image each hot spot. Protocols for automated image analysis were developed
using CellProfiler software. Clinical parameters of interest included grade, tumor palpability, comedo
necrosis, hormone receptor status, HER2 status, Ki67, recurrence, and Van Nuys score, (12 point scalemargins, age, size, grade). Associations were identified with non-parametric Spearman correlation test.
Summary: Immune infiltrates tended to be correlated with high risk DCIS features (high VNPI,
palpability, high grade, comedo necrosis, high proliferation, HER2-positivity, and HR-negativity). CART
analysis yielded a classifier composed of two markers: CD8+HLADR+ T cells and CD115 expression on
tumor cells. High CD115 expression on tumor cells predicted recurrence, as did low CD115 expression
combined with low CD8+HLADR+ T cells. In contrast, low CD115 expression on tumor cells along with
high numbers of CD8+HLADR+ T cells predicted good outcomes. Manipulation of the immune
microenvironment in DCIS, via local stimulation of the immune system, depletion of Treg, and/or
manipulation of macrophages could potentially alter disease progression.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(7)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #7
Evaluation of an cell-line derived signature of olaparib response (PARPi-7) as a predictive
biomarker of response to veliparib/carboplatin plus standard neoadjuvant therapy in high-risk
breast cancer: results from the I-SPY 2 TRIAL
Denise Wolf, Christina Yau, Ashish Sanil, Anneleen Daemen, Laura Heiser, Joe Gray, Lamorna BrownSwigart, Susan Flynn, Gillian Hirst, I-SPY 2 TRIAL Investigators, Meredith Buxton, Angela DeMichele,
Nola Hylton, Fraser Symmans, Doug Yee, Melissa Paoloni, Laura Esserman, Don Berry, Hope Rugo,
Olufunmilayo Olopade, Laura van ‘t Veer
Presenting Author:
Denise Wolf
Department of Laboratory Medicine
[email protected]
Abstract
Background: We developed a 7-gene DNA-repair deficiency signature (PARPi-7) that predicts breast
cancer cell line sensitivity to the PARP inhibitor olaparib. In the I-SPY 2 TRIAL, HER2- patients were
randomized to receive chemotherapy or the oral PARP inhibitor veliparib in combination with carboplatin
(V/C) and chemotherapy. V/C graduated in the triple-negative (TN) signature. Here we assess the
PARPi-7 as a specific biomarker of V/C response.
Methods: 115 HER2- patients (V/C: 71 and concurrent controls: 44) were considered in this analysis.
The PARPi-7 High/Low classification is computed from Agilent 44K array data as published using
expression levels of BRCA1, CHEK2, MAPKAPK2, MRE11A, NBN, TDG, and XPA. We assess
association between PARPi-7 and response in the V/C and control arms alone using Fisher’s exact test,
and relative performance between arms (biomarker x treatment interaction, likelihood ratio p < 0.05)
using a logistic model. This analysis is also performed adjusting for HR status as a covariate. To assess
PARPi-7 in the context of the graduating signature, we modify the Bayesian model used in I-SPY 2 to
include PARPi-7 status to estimate the predictive probability of V/C demonstrating superiority to control
in a 1:1 randomized phase 3 trial of 300 TN and/or PARPi-7 High patients. Our study is exploratory with
no claims for generalizability, and does not adjust for multiplicities of other biomarkers outside this study.
Results: In the V/C arm vs. concurrent controls, there were 62 PARPi-7 Low and 53 PARPi-7 High
patients, 26% of whom are HR+. The PARPi-7 High/Low classification associates with patient response
in the V/C arm (OR = 6.6, p=0.004) but not in the control arm (OR = 0.95, p=1). There is a significant
biomarker x treatment interaction (p=0.033), which remains upon adjusting for HR status (p= 0.028).
Examining the PARPi-7 in the context of the graduating TN signature, if the PARPi-7 is used to refine
the ‘biomarker-positive’ group by including only TN patients who are also PARPi-7 High, the predicted
probability of success in a 300-pt phase 3 trial is 99%, with estimated pCR rates of 69% in the V/C arm
vs. 25% in control, but this improved performance is at the expense of excluding 34% of the TN
population. Whereas if the PARPi-7 is used to expand the population by adding HR+/Her2-/PARPi-7
High patients to the TN group, the probability of phase 3 success is 94%, which is comparable to the
graduating signature (95%), while increasing the prevalence of biomarker-positive patients by 25% of
HR+/Her2- patients in the trial.
Conclusion: Our analysis suggests the PARPi-7 signature predicts response to veliparib/carboplatin
combination therapy relative to control. If verified in a larger trial, this signature may contribute to the
selection criteria of future PARP inhibitor trials, and be used in a single-sample response predictor
matching patients to treatments.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #8
I-SPY 2 Qualifying Biomarker Evaluation (QBE): The Challenge and Opportunity for Interrogating
Predicted Pathways in an Adaptive Design Biomarker Rich Trial
Christina Yau, Denise Wolf, Ashish Sanil, Laura van ’t Veer, Emanuel F Petricoin, Meredith Buxton, Joe
Gray, Angela DeMichele, Mike Hogarth, Nola Hylton, Jane Perlmutter, Melissa Paoloni, Fraser
Symmans, Doug Yee, Don Berry, Laura Esserman
Presenting Author:
Christina Yau
Buck Institute for Research on Aging, Novato
UCSF Department of Surgery
[email protected]
Abstract
I-SPY 2, a multicenter phase 2 neoadjuvant trial in high-risk breast cancer, uses adaptive
randomization within biomarker subtypes to evaluate novel agents added to standard chemotherapy. In
addition to efficiently evaluating agent/signature pairs, I-SPY 2 is a biomarker rich trial, where samples
are profiled for gene expression, protein levels, and mutation status. Biomarkers are classified as
established, qualifying, or exploratory. Established biomarkers are those used clinically (HR/HER2
status) or FDA cleared (MammaPrint), and,used for adaptive randomization to generate the 10
signatures from which a drug can graduate. Qualifying biomarkers (QB) represent evidence-based,
biologic pathway markers (e.g.cell line predictors, known drug targets). QB analyses must be prespecified and performed under CLIA. Exploratory markers are for discovery and may allow integration
of data from different technologies.
The QBE goal is to (1) evaluate biomarkers related to an agent’s mechanism of action to identify
promising candidates for testing/patient selection in future trials, and (2) create a resource to elucidate
biological mechanisms of response.
The wealth of biomarker data is both a boon and a challenge. Our small size limits the generalizability
of our findings. There are multiple genes in each pathway measured on multiple platforms, creating the
problem of multiplicity, which is compounded by the evaluation of multiple proposals. Biomarkers may
correlate with HR/HER2/MP subtypes. The adaptive randomization may increase the prevalence of
biomarker positive subsets and bias our findings. These challenges limit definitive conclusions, so our
statistics are descriptive rather than inferential, and are intended to avoid adding to the false positive
biomarker literature.
Methods: Three filters are applied: 1-The difference in biomarker performance in the experimental vs
control arm (biomarker x treatment interaction) is evaluated using a logistic model under a pre-specified
analysis plan 2-Biomarkers with a treatment interaction are dichotomized. The QB-High group is added
to the graduating subtype to define a novel signature and the treatment effect in this group is evaluated
3-If the treatment effect is comparable to the graduating signature, and the prevalence is increased, the
I-SPY 2 Bayesian model is modified to include the QB to assess the novel signature.
QBE to date: Veliparib in combination with carboplatin (V/C) and neratinib (N) are the first two agents to
graduate from I-SPY 2. For V/C, we have completed initial evaluation for 5 biomarker proposals,
including BRCA1/2 germline mutations and expression signatures associated with DNA repair
deficiencies. For N, 6 biomarker proposals, including HER family protein signaling markers, have been
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(9)
2015 UCSF Breast Oncology Program Scientific Retreat
assessed. Evaluation of the best candidates from these initial analyses in the I-SPY 2 Bayesian
framework is ongoing. Mutational analyses are pending.
Conclusions: We have developed a rigorous approach for QB analysis. A small number of QB warrant
further assessmsent. However, I-SPY 2 QB require validation, and should be considered preliminary
efforts to effectively screen QB candidates for evaluation in ongoing and future trials.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
(10)
2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #9
MammaPrint High1/High2 risk class as a biomarker of response to veliparib/carboplatin plus
standard neoadjuvant therapy for breast cancer in the I-SPY 2 TRIAL
Denise Wolf, Christina Yau, Ashish Sanil, Jo Chien, Anne Wallace, Angie DeMichelle, Hank Kaplan,
Doug Yee, Claudine Isaacs, Kathy Albain, Rebecca Viscuzi, Judy Boughey, Stacey Mulder,Steven
Chui, Qamar Khan, Toncred Styblo, Kirsten Edmiston, Donald Northfelt, Anthony Elias, Barbara Haley,
Debu Tripathy, Lamorna Brown-Swigart, Susan Flynn, Gillian Hirst, I-SPY 2 Executive Committee,
Hope Rugo, Olufunmilayo Olopade, Laura van ‘t Veer
Presenting Author:
Denise Wolf
Department of Laboratory Medicine
[email protected]
Abstract
Background: Further stratification of the 70-gene MammaPrintTM signature into ‘high’ and ‘ultra-high’
risk groups may help predict chemo-sensitivity. In I-SPY 2, patients were classified as MammaPrint
High1 (MP1) or MammaPrint (ultra) High2 (MP2), with MP2 defined as MP_score <-0.154. MP1/2
classification was added to HR and Her2 to define the cancer subtypes used in the I-SPY 2 adaptive
randomization engine. HER2- patients were randomized to receive chemotherapy or the oral PARP
inhibitor veliparib in combination with carboplatin and chemotherapy (V/C). V/C graduated in the triplenegative (TN) signature, where MP1/2 was not an eligible signature for graduation. Here, we assess
the performance of MP1/MP2 class as a specific biomarker of response to V/C.
Methods: 115 HER2- patients (V/C: 71 and concurrent controls: 44) were considered in this analysis.
We assess association between MP1/2 and response in the V/C and control arms alone using Fisher’s
exact test, and relative performance between arms (biomarker x treatment interaction, likelihood ratio p
< 0.05) using a logistic model. This analysis is also performed adjusting for HR status as a covariate.
To assess MP1/2 in the context of the graduating signature, we use the Bayesian model used in I-SPY
2 to estimate the predictive probability of V/C demonstrating superiority to control in a 1:1 randomized
phase 3 trial of 300 TN and/or MP2 patients. Our study is exploratory with no claims for
generalizability, and does not adjust for multiplicities of other biomarkers outside this study.
Results: In the V/C arm vs. concurrent controls, there were 66 MP1 (V/C: 32, Control: 34) and 49 MP2
patients (V/C: 39, Control: 10), 78% of which are TN. The OR between MP1/2 risk groups for predicting
pCR is 9.71 in the V/C arm (p=6.63E-05), in comparison to an OR of 0.97 in the control arm (p=1).
There is a significant biomarker x treatment interaction (p=0.023), which remains upon adjusting for HR
status (p= 0.028). Examining MP1/2 in the context of the graduating TN signature, if MP1/2 is used to
refine the ‘biomarker-positive’ group by including only TN patients who are also MP2, the predicted
probability of success in a 300-pt phase 3 trial is 97%, with estimated pCR rates of 66% in the V/C arm
vs. 25% in control, but this improved performance is at the expense of excluding 36% of the TN
population. Whereas if MP2 is used to expand the population by adding HR+/Her2-/MP2 patients to
the TN group, the probability of phase 3 success is 88%, which is comparable to the graduating
signature in this model (89%), while increasing the prevalence of biomarker-positive patients by 25% of
HR+/Her2- patients in the trial.
Conclusion: Our exploratory analysis suggests that MP2 suggests higher sensitivity to V/C combination
therapy relative to controls. This observation has prompted an investigation into the biological
mechanisms distinguishing the MP1/2 subtype that may account for this specificity.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #10
Evaluation of a BRCAness signature as a predictive biomarker of response to veliparib/
carboplatin plus standard neoadjuvant therapy in high-risk breast cancer: results from the
I-SPY 2 TRIAL
AM Glas1, J. Peeters1, C. Yau2, D.M. Wolf2, A. Sanil3, Y. Li1, T. Severson5, S. Linn5, I-SPY 2 TRIAL
Investigators6, M. Buxton2, A. DeMichele7, N. Hylton2, F. Symmans8, D. Yee9, M. Paoloni6, L.
Esserman2, D. Berry3, H. Rugo2, O. Olopade10, L.J. van 't Veer2
Author Affiliations:
1 Agendia
2 UCSF
3 Berry Consultants LLC
5 NKI
6 QuantumLeap
7 University of Pennsylvania,
8 The University of Texas MD Anderson
9 University of Minessota
10 University of Chicago
Presenting Author:
Christina Yau
Buck Institute for Research on Aging, Novato
UCSF Department of Surgery
[email protected]
Abstract
Background: We developed a 77-gene BRCAness gene expression signature that predicts 'BRCA1-like'
(vs. 'Sporadic-like') breast cancers with a validated high sensitivity and specificity rate. The BRCAness
signature was developed as part of the RATHER project (EU#258967). We hypothesized that BRCA1like tumors would have a higher sensitivity to PARP inhibitors, including veliparib. In the I-SPY II TRIAL,
HER2- patients were randomized to receive standard chemotherapy or the oral PARP inhibitor veliparib
in combination with carboplatin and chemotherapy (V/C). V/C graduated in the triple-negative (TN)
signature. Here we assess the BRCAness signature as a specific biomarker of V/C response.
Methods: 115 HER2- patients (V/C: 71 and concurrent controls: 44) were considered in this analysis.
The BRCAness classification is computed from Agilent full genome array data of the 77 signature
genes using our validated Diagonal Linear Discriminant Analysis (DLDA) model. We assess association
between BRCAness classification and response in the V/C and control arms alone (Fisher Exact test),
and relative performance between arms (biomarker x treatment interaction, likelihood ratio test) using a
logistic model. Our study is exploratory with no claims for generalizability of the data; and our statistical
calculations are descriptive. To assess the BRCAness signature in the context of the graduating TN
signature, we added the BRCA-like patients to the graduating TN subset and evaluated the predictive
probability of V/C demonstrating superiority to control in a 1:1 randomized phase 3 trial of 300 patients
from this new 'biomarker-positive' group in a modified I-SPY 2 Bayesian model. Our analyses do not
adjust for multiplicities of other biomarkers in the trial but outside this study.
Results: Of the 115 patients assessed, 56 are classified as BRCA-like. 16% of BRCA-like patients are
HR+HER2-. The BRCAness signature classification associates with patient response in the V/C arm
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
(OR = 6.8, p=0.0005) but not in the control arm (OR = 0.75, p=1). The p value is 0.018 for biomarker x
treatment interaction (OR in V/C arm relative to control arm = 9.3). This p value is 0.016 upon adjusting
for HR status. When the BRCA1-like patients are added to the graduating TN subset, our Bayesian
analysis suggests that the probability of V/C demonstrating superiority to control in a 300-patient 1:1
randomized phase 3 trial is 94%, which is comparable to the graduating TN signature (95% in this
modified model), while increasing the prevalence of biomarker-positive patients by ~8%.
Conclusion: Despite our small sample size, our pre-specified analysis suggests the BRCAness
signature is associated with response to veliparib/carboplatin combination therapy relative to control. All
I SPY 2 qualifying biomarker signatures require validation in larger trials prior to consideration to assist
in patient selection of future PARP inhibitor trial.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Detection and Biomarkers Poster #11
Evaluation of HER family protein signaling network as a predictive biomarker for pCR for breast
cancer patients treated with neratinib in the I-SPY 2 TRIAL
Julia D Wulfkuhle, Christina Yau, Denise M Wolf, Isela Gallagher, Ashish Sanil, Lamorna BrownSwigart, Susan Flynn, Gillian Hirst, I-SPY 2 TRIAL Investigators, Meredith Buxton, Angela DeMichele,
Nola Hylton, Fraser Symmans, Laura van ‘t Veer, Doug Yee, Melissa Paoloni, Laura Esserman, Don
Berry, Minetta Liu, John W Park, Emanuel F Petricoin
Presenting Author:
Denise Wolf
Department of Laboratory Medicine
[email protected]
Abstract
Background: We hypothesize that response to the pan-ERBB inhibitor, neratinib (N), may be predicted
by pre-treatment HER2-EGFR signaling. In the I-SPY II TRIAL, N graduated in the HR-HER2+
signature. All patients received at least standard chemotherapy. For HER2+ patients, N was
administered in place of trastuzumab. We evaluated 18 HER family signaling proteins as biomarkers of
N response using reverse phase protein microarray (RPMA) data from pre-treatment LCM purified
tumor epithelium.
Methods: 168 patients (N: 106, concurrent controls: 62) had RPMA and pCR data. 18 biomarkers
relating to HER family signaling were evaluated: AKT S473, AKT T308, EGFR, EGFR Y1068, EGFR
Y1148, EGFR Y1173, EGFR Y992, ERBB2, ERBB2 Y1248, ERBB3 total, ERBB3 Y1289, ERK1/2
T202/Y204, Heregulin, mTOR, mTOR S2448, PI3K p85 Y458/p55 Y199, PTEN S380, and SHC
Y317. We assessed association between biomarker and response in the N and control arms alone
(likelihood ratio test), and relative performance between arms (biomarker x treatment interaction) using
a logistic model. Analysis was also performed adjusting for HR/HER2 status. In an exploratory
analysis, we selected the marker with the greatest interaction (phosphorylated EGFR (Y1173)) to
dichotomize patients optimally based on the data and assessed it in the context of the graduating
signature by adding the EGFR Y1173-High patients to the HR-HER2+ subtype and evaluating the
predictive probability of V/C demonstrating superiority to control in a 1:1 randomized phase 3 trial of
300 patients from this new 'biomarker-positive' group in a modified I-SPY 2 Bayesian model. Our study
does not account for multiplicities or claim generalizability of the data. Statistical calculations are
descriptive rather than inferential.
Results: 7 HER pathway markers (EGFR Y1068, EGFR Y1173, EGFR Y992, ERBB2 total, ERBB2
Y1248, ERBB3 Y1289, SHC Y317) are associated with response in the N but not the control arm.
However, the difference in performance between arms did not reach significance by permutation
testing. Adjusting for HR/HER2 status, EGFR Y1173 shows a significant biomarker x treatment
interaction (p = 0.049). In an exploratory analysis, we dichotomized patients by their EGFR Y1173
levels (60 EGFR Y1173-Low, 108 EGFR Y1173-High). When EGFR Y1173 High patients are added to
the graduating HR-HER2+ subset, the predicted probability of Phase III trial success is 90%, which is
comparable to that for the graduating signature alone, while increasing the prevalence of biomarkerpositive patients by ~50%.
Conclusion: Our sample size is too small to draw definitive conclusions. Our exploratory analysis
reveals that HER family phosphoproteins associate with response to N, but only phosphorylated EGFR
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
(Y1173) appears to add value to the graduating signature. Given that this biomarker would expand the
patient population that may benefit, it merits evaluation in other ongoing trials of neratinib.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Epidemiology and Population Sciences Poster #1
Possible later age of breast cancer onset for Hispanic BRCA1 carriers with the protective
rs140068132-G allele
Laura Fejerman1*, Jeffrey Weitzel2*, Esther M. John3, C Villarreal2, Gary Unzeitig2, Darling Horcasitas2,
Charite Ricker2, Adrian Daneri2, Kayla Castaneda2, Alexander Miron3, Ana Maria Tuazon4, Magdalena
Echeverry4, Pilar Carvallo5, Carolina Alvarez5, Teresa Tapia5, COLUMBUS CONSORTIUM, Luis
Carvajal-Carmona6^, Susan Neuhausen7^+, Elad Ziv1^+
* These authors contributed equally to the study
^ These authors contributed equally to the study
+ Co-corresponding authors
Author Affiliations:
1 Department of Medicine, Division of General Internal Medicine, Institute of Human Genetics,
Comprehensive Cancer Center, University of California San Francisco, San Francisco CA 94158
2 Division of Clinical Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
3 Cancer Prevention institute of California, Fremont, CA 94538 and Division of Epidemiology,
Department of Health Research and Policy, Stanford University School of Medicine, Palo Alto, CA
94305
4 Facultad de Ciencias y de Ciencias de la Salud, Universidad del Tolima, Colombia
5 Department of Cell and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad
Católica de Chile
6 Department of Biochemistry and Molecular Medicine, University of California Davis, Davis CA 95616
7 Cancer Control and Population Sciences Program, City of Hope Comprehensive Cancer Center,
Duarte, CA 91010
Presenting Author:
Laura Fejerman
Department of Medicine, Division of General Internal Medicine
Institute of Human Genetics and Comprehensive Cancer Center
[email protected]
Abstract
Hispanic women in the U.S. have lower incidence of breast cancer compared to Non-Hispanic Whites
(NHW). A genome-wide association study (GWAS) of breast cancer in Hispanics reported a protective
variant near the ESR1 gene, only observed among women with Indigenous American ancestry
(rs140068132-A/G). The study also reported lower mammographic density among women who were
homozygous for the Indigenous American variant (G) and a stronger protective effect for estrogen
receptor negative breast cancer. In the present study, we assessed if this variant had an effect on age
at breast cancer diagnosis among Hispanic BRCA1 carriers, who commonly present with ER- disease.
We combined data from four studies of Hispanic BRCA1 mutation carriers with breast cancer: the
Clinical Cancer Genetics Community Research Network (CCGCRN; N=152), Northern California Breast
Cancer Family Registry (NC-BCFR, N=27), and two studies in Latin America, one from Colombia
(N=33) and one from Chile (N=27). We used a non-parametric Kruskal-Wallis equality-of-populations
rank test to evaluate if the age of breast cancer diagnosis was associated with the rs140068132
polymorphism among BRCA1 carriers. We conducted separate analyses of Hispanic women from
California and women from Colombia and Chile. Among 239 BRCA1 carriers, we observed 201
homozygous AA, 36 heterozygous, and 2 missing genotypes, with an overall allele frequency of the G
allele of 7.6%. We did not find a statistically significant effect of rs140068132 on age at diagnosis
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
among Hispanic BRCA1 carriers overall. However, we found a suggestion of later age at diagnosis,
with median age at diagnosis of 39.8 years (33-46 years) in AA homozygous compared to 44 years (3450 years) in heterozygous (p value=0.1) women from California. We did not observe an association
among the patients from Colombia and Chile. Studies of BRCA mutation carriers are often limited by
selection for breast cancer cases, thus there may be a bias against enrollment of BRCA carriers with
the protective allele in the present analysis. The observed suggestion of a difference in age at
diagnosis in the samples from California, similar to genome-wide identified variants that have been
shown to have an effect among BRCA1 and BRCA2 carriers, warrants further investigation.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Epidemiology and Population Sciences Poster #2
Alcohol Consumption and Mortality after Breast Cancer Diagnosis: the Health and Functioning
in Women Study
Natasha Din MD1, Isabel Elaine Allen PhD2, Dejana Braithwaite PhD3
Author Affiliations:
1 Clinical research fellow, Department of Epidemiology and Biostatistics, UCSF
2 Professor, Department of Epidemiology & Biostatistics
3 Associate Professor, Department of Epidemiology & Biostatistics and Helen Diller Family
Comprehensive Cancer Center, UCSF
Presenting Author:
Natasha Din
Epidemiology & Biostatistics
[email protected]
Abstract
Objective: To determine the effects of alcohol consumption on long-term mortality from breast cancer
and other causes among a cohort of women with breast cancer.
Methods: Patients included were 939 women, aged 40-84 years, with breast cancer recognized within
the Metropolitan Detroit Cancer Surveillance System (MDCSS) and were followed for a median followup of 11 years in the U.S, Health and Functioning in Women (HFW) study. Alcohol consumption was
assessed by a questionnaire and information about type, amount and intensity of alcohol intake was
ascertained. The risk of death from breast cancer and other causes reported in the first few months
following breast cancer diagnosis were estimated using Cox proportional hazard models.
Results: During a median follow-up of 11 years from diagnosis, 724 deaths occurred overall, with 303
from breast cancer. 55% were considered drinkers. We found that in low and moderate volume alcohol
drinkers, the hazards of mortality due to causes other than breast cancer decreased significantly (H.R,
0.61; 95% C.I, 0.47-0.78; H.R, 0.57; C.I: 0.39-0.85). Additionally, low frequency (0.75-3.75 drinks/week)
of alcohol intake, decreased risk of other-cause mortality significantly in beer and wine drinkers in
covariate adjusted models alike (H.R, 0.69; 95% C.I, 0.50-0.96; H.R, 0.68; 95% C.I, 0.52 to 0.88). With
other alcohol drinks, high intake (10.5-36 drinks/week) was seen to decrease risk of other cause
mortality significantly (H.R, 0.54; 95% C.I, 0.31 to 0.95). No such significant association was found
among beer, wine and other alcohol drinkers with breast cancer specific mortality. On stratifying with
tumor stage, a similar decrease in other cause mortality was seen with local stage of breast cancer at
diagnosis and low intake of wine (H.R, 0.64; 95% C.I, 0.45 to 0.89). Other cause-mortality also had a
trend towards decrease with low intake of beer, wine and other alcohol drinks and regional and distant
stage of breast cancer at diagnosis. Furthermore, we observed a marginally statistically significant
interaction between alcohol intake and current smokers (H.R, 1.72; 95% C.I, 0.97 to 3.05, P
interaction=0.06).
Conclusion: Our findings indicate that light to moderate alcohol consumption at the time of breast
cancer diagnosis is associated with decreased risk of other-cause mortality and is weakly associated
with breast cancer specific mortality. Further studies with broader range of alcohol consumption and
longer follow-up will help to clarify the relationship.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #1
Hypoxia induces resistance to endocrine therapy
Mercè Padró1, Raymond J. Louie1, Brian V. Lananna1, Luika A. Timmerman2, Adam J. Krieg3, and
Denise A. Chan1.
Author Affiliations:
1 Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
94115, USA
2 Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San
Francisco, San Francisco, CA 94115, USA
3 Department of Obstetrics and Gynecology, Kansas University Medical Center, Kansas City, KS
66160, USA
Presenting Author:
Merce Padro Jove
Radiation Oncology
Denise Chan Lab
[email protected]
Abstract
De novo and acquired resistance to cancer treatments are major challenges that lead to poor, clinical
outcomes. Tumor hypoxia, or conditions of low oxygen, is a prominent mechanism for resistance to
standard therapies, including radiation therapy and chemotherapy. However, the role of hypoxia in
endocrine therapy response has not been thoroughly investigated. We demonstrate that hypoxia, by
repressing the estrogen receptor, plays a direct role in response to endocrine therapy in estrogen
receptor-positive breast cancers. Our data indicate that hypoxia selects for cells that can grow
independently of estrogen signaling, have a more aggressive phenotype, and are resistant to endocrine
therapy. Furthermore, our analysis of clinical data reveals that estrogen receptor-positive breast cancer
patients treated with tamoxifen with a high hypoxic signature had reduced survival compared to those
patients treated with tamoxifen with a low hypoxic signature, indicating that hypoxia may be a
mechanism leading to endocrine therapy resistance. Taken together, these findings suggest that
hypoxia acts as a physiological relevant stress that negatively influences the response to endocrine
therapy.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #2
Targeting HER3 by interfering with its Sec61-mediated cotranslational insertion into the
endoplasmic reticulum
Ana Ruiz-Saenz1, Manbir Sandhu1, Yazmin Carrasco2, Rebecca L. Maglathlin2, Jack Taunton2,3, Mark
M. Moasser1
Author Affiliations:
1 Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California,
San Francisco, San Francisco, CA, USA;
2 Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San
Francisco, CA, USA
3 Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
Presenting Author:
Ana Ruiz-Saenz
Medicine. Division of Hematology/Oncology
[email protected]
Abstract
There is increasing evidence implicating HER3 in several types of cancer, as a resilient copartner for
HER2 in HER2-amplified cancers, and as a driver of resistance in many other types of cancer.
However, the development of targeted therapies to inactivate HER3 function has been a challenging
endeavor. Its tumor-driving functions are only sometimes driven by ligand-activation, and targeting its
extracellular domain with antibody molecules has only limited effects. Its kinase domain functions in
allostery, not catalysis, and we have previously shown that the classical ATP-analog class of tyrosine
kinase inhibitors fail to inactivate it. Here we describe a novel approach that eliminates HER3
expression. This involves interfering with mechanisms critical for its cotranslational translocation into
the endoplasmic reticulum (ER), resulting in the elimination of HER3 protein expression and loss of
HER3 function. The small-molecule cotransin CT8 binds the Sec61 translocon channel in the ER
membrane and prevents the signal peptide of the nascent HER3 protein from initiating its
cotranslational translocation into the lumen of the ER, resulting in the degradation of HER3.
Interestingly, CT8 treatment prevents HER3 translocation while the other HER proteins are unaffected.
In addition, CT8 treatment suppresses the compensatory induction of HER3 that accompanies lapatinib
treatment of HER2-amplified cancer cells, making for a durable suppression of HER2-HER3 signaling
with the lapatinib-CT8 combination. Consistent with the effective inactivation of HER2-HER3 signaling,
CT8 treatment synergistically enhances the apoptotic effects of lapatinib in HER2-overexpressing
cancer cells. The target selectivities of cotransins are highly dependent on their structure and the signal
sequence of targeted proteins and can be narrowed through structure-function studies. Our results thus
highlight Sec61-dependent processing as a novel strategy to eliminate HER3 expression and function
with considerable potential for the treatment of HER2-amplified and other types of cancers.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #3
Age-dependent epigenetic regulation of BRCA1 in human mammary epithelium
E. Lorena Mora-Blanco, Masaru Miyano, Yi-Hsuan Fu, Sylvain Costes, and Mark A. LaBarge
Author Affiliation:
Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Presenting Author:
Lorena Mora-Blanco
Lawrence Berkeley National Labs
[email protected]
Abstract
The greatest risk factor for cancer is aging; 70% of breast cancers (BC) are diagnosed in persons aged
55 and older. However, little is known how aging alters susceptibility at the cellular and molecular levelincluding stem cell potential. The breast is a bi-layered secretory epithelium whose basic unit is the
terminal ductal lobule unit, an arbor-like structure with a contractile myoepithelial (MEP) outer layer,
secretory luminal epithelial (LEP) interior and interspersed multipotent progenitors (MPP). MEPs are
thought to be tumor-suppressive, while MPP are putative etiological roots of BCs. MPP in older women
acquire differentiation defects and give rise to LEP that express proteins normally only associated with
basal/myoepithelial cells in younger women. We have demonstrated that the aging process in breast is
associated with accumulation of defective MPP and LEP, and a decrease in the MEP cell population.
Normal mammary epithelia from women over 55 years old and 30-something non-tumor breast tissues
of BRCA1 mutation carriers (who have >90% lifetime risk of breast cancer) share a similar phenotype
of expanded progenitor pools and basal-biased stem cell differentiation patterns, suggesting it may be a
general phenotype of epithelia that are susceptible to malignant transformation. It has been well
established that DNA methylation increases with age, although the tissue-specific functional relevance
has not been addressed. Investigating the epigenetic changes in the regulation of key breast
homeostasis regulators like BRCA1 in the mammary epithelium will not only improve our understanding
of changes in regulation as cells chronologically age, but also may provide insight for the molecular
mechanisms responsible for the increase in BC susceptibility as women age.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #4
Comprehensive molecular profiling of circulating tumor cells from metastatic breast cancer
patients
Mark Jesus M. Magbanua, Louai Hauranieh, Ritu Roy, Praveen Pendyala, Eduardo V. Sosa, Janet H.
Scott, Hope S. Rugo and John W. Park
Presenting Author:
Mark Jesus Magbanua
Hem/Onc
[email protected]
Abstract
Background: Recent enumeration studies on CTCs have demonstrated the clinical value of these cells.
The molecular biology of CTCs, however, remains poorly understood.
Methods: We performed RNA and DNA profiling of CTCs from metastatic breast cancer (MBC)
patients. 244 blood samples from 162 MBC patients were subjected to immunomagnetic enrichment
and fluorescence activated cell sorting (IE/FACS) to isolate highly pure CTCs. Microfluidic-based
multiplex QPCR analysis was utilized to determine the expression levels of 64 cancer-related genes.
Parallel genome-wide copy number analysis by array comparative genomic hybridization was also
performed on CTCs isolated from the same enriched blood samples.
Results: Transcriptional analysis of CTCs was successfully performed in 151 samples from 105
patients. We observed the up-regulation of several genes including CCND1, EPCAM, KRT7 and MUC1
and the down-regulation of hematopoietic-related genes including PTPRC (CD45) and CD68 (adjusted
p <0.001) in CTCs. Clustering analysis of expression profiles revealed three CTC clusters, one
containing both subtypes basal (ESR1-low) and normal-like (ESR1-low, CAV1/VIM-high) and two other
clusters containing luminal subtype (ESR1-high). A subset of CTCs expressed epithelial-mesenchymal
transition genes, however, genes for stem cellness were not generally expressed. Serial CTC
expression profiling in 28 patients demonstrated changes in expression over time. Exploratory single
CTC expression analysis revealed cell-to-cell heterogeneity. Parallel genome-wide copy number
analysis in matched CTCs from 49 patients revealed gains (e.g. 1q and 8q), losses (e.g., 8p and 16q),
and focal amplifications (e.g. on 8q and 11q including CCND1) that are frequently observed in primary
breast cancers. We also observed three copy number clusters with varying levels of genomic
aberrations. Up-regulation of CCND1 and ERBB2 in CTCs was associated with increased level of
genomic instability.
Conclusions: Parallel gene expression and copy number profiling provided novel insights on the biology
of CTCs. Molecular characterization of CTCs may shed further light on the biology of metastasis and
disease progression.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #5
A novel NAMPT inhibitor is effective against breast and ovarian cancer cells
Christine Janson, Merce Padro Jove, Breanna Luna, Denise Chan
Author Affiliation:
UCSF, Radiation Oncology
Presenting Author:
Christine Janson
Radiation Oncology
[email protected]
Abstract
Under normal oxygen and growth conditions, cells use aerobic respiration to produce ATP. When cells
experience hypoxia (low oxygen levels) they can undergo a metabolic switch and utilize glycolysis to
produce ATP. Cancer cells can permanently switch to glycolysis for energy production even in
normoxia (physiological oxygen levels), a phenomenon known as the Warburg effect. Many renal
carcinoma cell lines (RCCs) have lost the expression of the von Hippel-Lindau (VHL) tumor suppressor,
which is important for the downregulation of Hypoxia Inducible Factor (HIFα), and are dependent on
aerobic glycolysis. Using a high-throughput chemical synthetic lethal screen, we identified compounds
that kill cells reliant on glycolysis. One class of compounds, the 7-series, is effective against breast and
ovarian cancer in vitro and in vivo. We determined the IC50 for RUG-70099 using XTT and clonogenic
assays, which determined the drug’s efficiency in the low nanomolar range. RUG-70099 also reduced
the size and number of metastatic lesions in a xenograft model of ovarian cancer. NAMPT is the ratelimiting enzyme in the NAD+ biosynthesis pathway, which is necessary for cellular metabolism. Using
an in vitro enzymatic assay with purified NAMPT, we determined that the drug can inhibit NAMPT
activity. Since the Warburg effect and upregulation of NAMPT is observed in many cancer types, this
compound will only selectively kill renal cancer cells but may also serve as a potential therapy for all
cancer types.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #6
Transcriptional and genomic approaches for characterization of disseminated tumor cells
Mark Jesus M. Magbanua, Rishi Das, Prithi Polavarapu, and John W. Park
Author Affiliation:
UCSF
Presenting Author:
Prithi Polavarapu
Hemotology Oncology
[email protected]
Abstract
Clinical studies have shown that the presence of disseminated tumor cells (DTCs) in the bone marrow
is associated with increased risk of distant metastasis and poor survival. Despite the known clinical
significance, the molecular nature of DTCs remains elusive. There is a paucity of studies focused on
molecular profiling of DTCs because the high cellularity and complexity of the bone marrow pose a
unique challenge in the isolation and direct characterization of these rare cells. In addition, the limited
amount of tumor DNA/RNA available for molecular interrogation further complicates efforts on genetic
characterization of DTCs. In this paper, we reviewed published scientific reports, spanning a decade
and half of research, describing the purification and genomic analysis of DTCs. Although few studies
exist, these seminal efforts provide the foundation that is vital to the current biological understanding of
DTCs. Further molecular characterization of DTCs may reveal novel insights into the mechanisms of
tumor evolution and disease progression, and may provide unique information that will enable the
development of new cancer therapies.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #7
Aging microenvironment imposes DNA methylation alterations, leading to loss of luminal
phenotype
Masaru Miyano, Jonathan K Lee, Mao Jian-Hua and Mark A. LaBarge
Author Affiliation:
Lawrence Berkeley National Laboratory
Presenting Author:
MASARU MIYANO
Lawrence Berkeley National Laboratory
[email protected]
Abstract
Aging is the greatest risk factor for breast cancer, although the cellular and molecular mechanism is
unknown. Age-dependent gene expression is known in several human tissues and, in the breast,
luminal epithelial cells (LEP) from women over 55 years old show loss of the lineage specific gene
expression. Epigenomic states, particularly DNA methylation patterns, also change in an agedependent manner. However, little is known regarding the mechanisms by which these age-associated
changes are introduced and the cellular/functional consequences of these alterations. Tissue
microenvironment plays an important role in the maintenance of cellular identity, including specific gene
expression profiles. Decreased connective tissues and disruption of extra-cellular matrix are observed
in aged breast, suggesting that chronological age is responsible for tissue-level microenvironmental
changes. In the human breast, age modulates tissue-level microenvironmental integrity, including
decreased connective tissues and disruption of extra-cellular matrix. Therefore, we hypothesize that
age-dependent phenotypic drift in the breast is driven by imposed epigenetic states via age-associated
microenvironmental changes.
To understand the molecular basis how microenvironment contributes to loss of LEP phenotype with
age, we have established the human mammary epithelial cells (HMEC) aging resources, a large and
genetically diverse group of normal, finite lifespan HMEC strains derived from women aged 16 to 91
years. Utilizing HMEC and a number of controlled microenvironmental conditions, we demonstrate that
LEP-specific gene expression is imposed by lineage-specific microenvironments. We identified that
age-dependent gene expression in LEP, which is characterized by a degree of loss of tissue-specificity,
was imposed by age-specific microenvironments. Promoter methylation patterns were dynamic, being
altered over time in accordance with microenvironment influence. Young-derived LEP adopted elderly
gene expression and methylation patterns when cultured in an aged microenvironment. Our approach
provides evidence that normal age-related microenvironment impacts cellular phenotype, which may
explain an increased susceptibility to breast cancer with age.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #8
MicroRNA signature in breast cancer linked to subtype and therapeutic drug response
Koei Chin1,2, Anneleen Daemen1,5, Laura Heiser2, Molly Klein-McDowell1, Andrei Goga1, Paul Yaswen4,
Chris Benz3 and Joe Gray2
Author Affiliations:
1 University of California San Francisco
2 Oregon Health and Science University
3 Buck Institute
4 Lawrence Berkeley National Laboratory, 5Genentech
Presenting Author:
Koei Chin
Laboratory Medicine
Biomedical Engineering
[email protected]
Abstract
A microRNA (miRNA) is an endogenous small non-coding RNA molecule (containing 19-25
nucleotides) found in plants, animals, and some viruses, which post-transcriptionally regulates gene
expression through RNA silencing. The miRNAs are involved in almost every biological process
including cell cycle regulation, cell growth, apoptosis, cell differentiation and stress response, therefore
play an important role in cancer progression and metastasis. Here we describe the signature of
aberrant miRNA expression in 40 breast cancer cell lines, associated with intrinsic molecular subtypes
in breast cancer and therapeutic drug response. We have profiled miRNA expression in 40 breast
cancer cell lines using multiplex RT-qPCR and found significant sets of 197 miRNAs that are
specifically up- or down-regulated in luminal subtype and basal-like subtype. Since these miRNAs may
modulate oncogenic or tumor suppressive signaling pathways to facilitate cellular proliferation and
survival, they are potentially therapeutic targets or prognostic biomarkers. For being further along in the
study, we explored the miRNA association with drug response in those cell lines threated with 97
therapeutic compounds, including 76 molecular targeting agents. We identified 175 miRNAs that show
aberrant expression and are associated with the response to molecular targeting agents. Especially
miR-196b, miR-21, miR-9, miR-146b, miR-30a-3p and miR-34b are involved in more than 10
compounds which spectra are quite random between miRNAs. One of our goals in this study is to
identify significant miRNA predictors for prediction of drug response. For miRNA selection, logistic
regression model was used with forward feature selection and Wilcoxon rank sum was also used to
identify significant miRNA (p-value). Per compound, the targets are selected of the miRNAs that satisfy
such two criteria: selected in 10 iterations, or selected in 3 iterations with average p-value < 0.01), and
the list of targets is further reduced to those targets that are associated with drug response with a pvalue <0.05 (Wilcoxon rank-sum test) using two expression data sets for the cell lines that we have
generated in the laboratory (i.e. Affymetrix U133A and Affymetrix exon array). Also we analyze targets
of relevant miRNAs using microRNA.org database.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #9
Data Integration to Identify Markers of Drug Response in Breast Cancer
James T Webber1, Nevan J Krogan2, Sourav Bandyopadhyay3
Author Affiliations:
1 Bioengineering & Therapeutic Science, UCSF
2 Cellular & Molecular Pharmacology, UCSF
3 Bioengineering & Therapeutic Science, UCSF
Presenting Author:
James Webber
Bioengineering & Therapeutic Science
Bandyopadhyay Lab
[email protected]
Abstract
Currently, treatment for breast cancer is determined by the use of clinical subtypes and a relatively
small number of molecular markers. While these subtypes are an effective way to classify patients, a
significant number of patients do not respond to the indicated treatment as expected. Moreover, many
patients do not have any clear oncogenic target and cannot be effectively treated. Thus there is a need
for more precise subtyping and for new biomarkers of drug sensitivity and response in breast cancer.
In this project, we are integrating multiple data types from two different breast cancer datasets--a
collection breast cancer tumors, and a panel of breast-cancer-derived cell lines. By finding gene
clusters that are differentially active across both tumors and cell lines, and then correlating these
clusters with drug response data, we will identify sets of genes that are both predictive of drug
sensitivity and also commonly activated in clinical samples.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #10
Elucidating the Synthetic Lethal Effect of CDK1 Inhibition in Triple Negative Breast Cancer
Julia Rohrberg, Alexandra Corella, Linda Starnes, Andrei Goga
Author Affiliation:
University of California, San Francisco, Cell and Tissue Department/Department of Medicine
Presenting Author:
Julia Rohrberg
Department of Cell and Tissue Biology
Department of Medicine
[email protected]
Abstract
Triple-negative breast cancer (TNBC) presents the most challenging breast cancer subtype with
the poorest outcome. No targeted therapeutic strategies are currently available for this subtype
due to limited insights into the mechanisms of tumorigenesis and tumor maintenance. Thus,
there is an urgent need to deepen our understanding of this disease and to identify clinically
relevant targets for therapeutic intervention. Our lab recently reported that the oncogenic MYC
pathways were disproportionally deregulated in primary human TNBC tumor samples and that
the MYC status predicted patients’ poor prognosis. Clinical development of small molecule
inhibitors for MYC transcriptional activity has not been successful during the past two decades
due to missing target sites. However, our lab identified a novel MYC-dependent synthetic-lethal
interaction in which inhibition of cyclin-dependent kinase 1 (CDK1) resulted in the selective
killing of MYC overexpressing cancer cells while sparing non-tumorigenic cells. This concept is
novel and has recently entered a Phase 1B trial for clinical evaluation at UCSF. However, the
inhibition of the only CDK1 that regulates a larger number of substrates might cause adverse
toxicity, which will limit clinical utility. Furthermore, the molecular mechanisms by which CDK1
inhibition induces MYC-dependent lethality are unknown. We hypothesize that the mechanism
of MYC-CDK1 synthetic lethality can be attributed to loss of function only in one or a handful of
the CDK1 substrates and that the inhibition of such specific CDK substrates is sufficient in
inducing MYC-dependent cell death.
To identify specific CDK1 substrates whose loss-of-function phenocopies CDK1 inhibition in
MYC-driven breast tumors I combined bioinformatics analysis of gene expression data from
patient samples and in vitro screening approaches. I identified five promising candidates, of
which TPX2 most efficiently killed MYC overexpressing cells while sparing normal nontumorigenic cells. Using analog-sensitive CDK1 we confirmed that TPX2 is a direct substrate of
CDK1.
Our study will not only expand our knowledge on the biology of TNBC but will also provide less
toxic and more efficacious targeted therapies for the patients with TNBC.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #11
Precting the Responses of Breast Cancer Cell lines to Drugs
Leslie C. Timpe, Ph.D., Dian Li, Ten-Yang Yen, Ph.D., Judi Wong, M.D., Roger Yen, Bruce A. Macher,
Alexandra Piryatinska
Author Affiliations:
Department of Mathematics
Department of Chemistry and Biochemistry
San Francisco State University
Presenting Author:
Leslie Timpe
San Francisco State University
[email protected]
Abstract
Background: Approximately 20 drugs have been approved by the FDA for use in breast cancer, yet
predictive biomarkers are known only for a few of them.
Results: The responses of breast cancer cell lines to over 80 drugs can be modeled quantitatively using
protein expression data collected by mass spectrometry or by reverse phase protein array. Candidate
predictor proteins were selected by lasso regression. Using 1-3 predictor proteins, we created
statistically significant regression models that fit the observed drug sensitivities of the breast cancer cell
lines to 86 of 90 drugs modeled, including drugs currently in use for breast cancer treatment, eg
paclitaxel, gemcitabine and vinorelbine, and for drugs in development, eg PI3K inhibitors or palbociclib.
Conclusion: The results show that the expression level of a small number of proteins measured by
mass spectrometry can predict quantitatively the sensitivities of breast cancer cell lines to a large
number of drugs. These proteins are candidate biomarkers for drug response in patients. The
approach is general; it can be applied to drugs in current use, or for patient selection for drugs in
development.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Molecular Biology Poster #12
Using Patient Derived Xenograft (PDX) and MYC-Driven Transgenic Models of Breast Cancer to
Identify Druggable Oncogenic Driver Mutations
Meng Li1, Alicia Zhou1, Devon Lawson2, Xiaosong Zhang1,3, Andrei Goga1,3
Author Affiliations:
1 Dept. Cell & Tissue Biology, University of California, San Francisco
2 Dept. of Anatomy, University of California, San Francisco
3 Dept. of Medicine, University of California, San Francisco
Presenting Author:
Meng Li
Cell and Tissue Biology
[email protected]
Abstract
Cancer is a genetic disease in which only 4-5 somatic mutations are sufficient to transform human cells.
However, cancer genome sequencing has discovered hundreds of driver-like mutations per tumor in
most adult solid cancers. The question becomes how to weigh and quantify the selective advantages of
individual cancer gene mutations and identify the most important cancer driver genes that are essential
for tumor growth and are therefore most efficacious to target. We have established a next generation
exome sequencing and analysis pipeline for both human patient derived xenograft (PDXs) and mouse
cancer models. We found that inactivating mutations in BRCA1 and BRCA2 genes were 8-fold enriched
in breast cancer PDXs and were associated with successful tumor engraftment in mice and poor clinical
outcomes of breast cancer patients. We also identified a novel mutation in the splicing factor SRSF2
that occurred in a breast cancer following chemotherapy treatment. This suggests that RNA splicing
machinery mutations may confer chemoresistance. In Myc-driven mouse breast cancer models, we
found that while slow growing Myc-driven breast tumors harbored one heterozygous PIK3R1
inactivating mutation, fast growing tumors harbored two heterozygous PIK3R1 inactivating mutations,
indicating that second hit PIK3R1 mutations significantly accelerated tumor growth in vivo. This finding
suggests that PIK3R1 may be a major cancer driver gene in the context of MYC over-expression, and it
may be an important target for cancer therapy. Our work lays the foundation for systematic functional
and phenotypic annotation of human breast cancer genes, and links cancer gene mutations to tumor
aggressiveness and chemoresistance phenotypes in vivo.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Physical Sciences Poster #1
High spatial resolution DTI sequence for characterizing breast tumor early treatment response:
preliminary comparison to standard DTI sequence
Lisa J Wilmes1, Wei Ching Lo1, David C Newitt1, Suchandrima Banerjee2, Evelyn Proctor1, Emine U
Saritas3, Ajit Shankaranarayanan2, Nola M Hylton1
Author Affiliations:
1 Department of Radiology and Biomedical Imaging, University of California, San Francisco, San
Francisco, CA
2 Applied Science Laboratory, GE Healthcare, Menlo Park, CA,
3 Department of Bioengineering, University of California, Berkeley, CA
Presenting Author:
Lisa Wilmes
Radiology and Biomedical Imaging
[email protected]
Abstract
Background: Diffusion-tensor magnetic resonance imaging (DTI) employs diffusion weighting gradients
to generate measures of both 1) the directionality of tissue water movement, such as fractional
anisotropy (FA) and 2) the magnitude of water mobility, or apparent diffusion coefficient (ADC). These
measures can provide information about tissue microstructure. A recent study of DTI found that FA was
significantly lower in breast tumors than in normal fibroglandular tissue, and that FA provided increased
diagnostic accuracy over ADC alone. To date there have been few of studies of treatment effects on
DTI parameters in breast cancer. One limitation of standard commercially available DTI sequences
(STD-DTI), is that the spatial resolution is generally not as high as that of other MRI sequences, which
may limit the ability of DTI to detect changes. In this work a high-resolution single-shot EPI reducedfield of view DTI acquisition (HR-DTI), with a 2D spatially-selective echo-planar RF excitation pulse,
was optimized for breast imaging and compared to a STD-DTI sequence for characterizing early
treatment changes in breast tumor FA and ADC in patients receiving neoadjuvant chemotherapy.
Methods: Seven patients with invasive breast cancer were scanned with both HR-DTI and STD-DTI
prior to treatment ad after one cycle of taxane based therapy as part of an ongoing IRB approved study
at our institution. Imaging was performed on a 1.5T GE Signa scanner. ADC and FA maps were
calculated for both acquisitions. Tumor ADC and FA values from the two sequences were compared
using a two tailed t-test and tumor volume change correlations between DTI parameters were assessed
with a Pearson’s correlation.
Results: HR-DTI tumor FA was significantly higher than STD-DTI for both time points, and this
difference increased at the early treatment time point. No significant differences in mean tumor ADC
were found. Of the DTI parameters, mean tumor HR-FA had the strongest correlation with tumor
volume change at the end of treatment.
Conclusion: This preliminary work suggests that HR-DTI FA may be more sensitive than STD-DTI FA to
early treatment related changes in breast tumors. The study is ongoing and will evaluate HR-DTI in a
larger number of breast cancer patients.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Physical Sciences Poster #2
Tissue tension promotes mammary stemness and breast cancer aggression
Jason J Northey1, Yoshihiro Yui1, Janna K Mouw1, Amanda C Wijekoon1, Jonathon N Lakins1, Valerie
M Weaver1-4
Author Affiliations:
1 Center for Bioengineering and Tissue Regeneration, Department of Surgery
2 Department of Anatomy and Department of Bioengineering and Therapeutic Sciences
3 Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research
4 UCSF Helen Diller Comprehensive Cancer Center
Presenting Author:
Jason Northey
Surgery
Weaver Lab
[email protected]
Abstract
Breast cancers frequently develop treatment resistance mechanisms that lead to recurrence,
dissemination and patient mortality. Among these mechanisms is the ability of tumor cells to undergo
an epithelial-to-mesenchymal transition (EMT) and exhibit stem-like behavior. Data from our laboratory
using preclinical models and clinical samples suggests that tissue tension increases prior to and
accompanies malignant transformation. Therefore, we hypothesize that enhanced tissue tension fosters
mammary stemness, EMT and breast cancer aggression. In order to enhance tissue tension in vivo, we
generated transgenic mice with conditional expression of a Beta1-Integrin clustering mutant (V737N) in
the mammary epithelium. V737N expression stimulated integrin-mediated mechanosignaling in
mammary epithelial cells (MECs), as determined by elevated phosphorylation of FAK and p130Cas,
and this heightened mechanosignaling promoted epithelial ductal branching, end bud formation and
proliferation in the mammary gland. Moreover, we discovered an increase in the ratio of
basal/myoepithelial to luminal MECs in V737N-expressing mammary glands. Isolated V737Nexpressing MECs contained higher expression of genes associated with EMT and stemness, and
colony formation and transplantation assays revealed a functional increase in progentior/stem cell
frequency in the V737N-expressing basal/myoepithelial MECs compared to their corresponding
Controls. Finally, to examine the effect of higher tissue tension on breast cancer progression, we
expressed the V737N-Beta1-Integrin together with a mouse model of HER2-positive breast cancer
(MMTV-NEU). While V737N-expression had no observable effect on primary tumor outgrowth, overall
tumor incidence and lung metastasis were significantly augmented. Further examination of tumors
uncovered a phenotypic shift, such that V737N-expressing tumors displayed expression patterns
resembling an EMT when compared to control tumors. Thus, tissue tension by way of enhanced
mechanosignaling promotes mammary stemness and a more basal-like aggressive mammary tumor
character.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Physical Sciences Poster #3
Global Profiling of Extracellular Proteolysis as a Molecular Stratification Tool for Breast Cancer
Michael B. Winter1, Natalia Khuri2, Giselle M. Knudsen1, Anthony J. O’Donoghue1, Andrej Sali2, Charles
S. Craik1
Author Affiliations:
1 Department of Pharmaceutical Chemistry, UCSF
2 Department of Bioengineering and Therapeutic Sciences, UCSF
Presenting Author:
Michael Winter
Pharm Chem
Craik Lab
[email protected]
Abstract
One of the hallmarks of aggressive breast cancer is its ability to spread to new tissues, a process that is
mediated in part by the activity of extracellular proteases. Protease activity is tightly regulated by
subcellular localization, the presence of endogenous protease inhibitors, and requisite conversion from
inactive precursor forms. Therefore, in these circumstances, it is not enough to know protease
expression levels alone. We propose that global profiles of extracellular protease activity may emerge
as a powerful functional tool for the stratification of breast cancer. We have developed a novel mass
spectrometry-based screening strategy that can identify the global substrate specificity and kinetic
efficiency of proteases alone and in complex biological mixtures by employing a small, diverse library of
rationally designed peptide substrates. This assay, referred to as Multiplex Substrate Profiling by Mass
Spectrometry (MSP-MS), marks a significant advance in protease profiling by allowing for the unbiased
and simultaneous detection of all protease activities in a given sample. To test the hypothesis that
global profiles of extracellular proteolysis can be used to stratify cancer samples, we have applied the
MSP-MS assay to measure total secreted protease activity from a panel of nine breast cancer cell lines
that correspond to previously defined molecular subtypes. Sampling of conditioned media revealed
distinct differences in proteolysis between invasive and non-invasive cell lines. Invasive cell lines were
found to exhibit markedly higher protease activity against the peptide library and display distinct global
substrate specificity profiles. Two-way clustering taking into account the residues flanking each
observed cleavage was used to group the cell lines on the basis of their global substrate specificities
and cleavage kinetics. Cell line clustering results obtained using this approach both supported and
expanded upon the expected stratification derived from traditional markers. Incorporation of classspecific protease inhibitors into the multiplex assay coupled with shotgun proteomics analysis is being
used to assign the dominant activities observed to specific cancer-associated proteases. We anticipate
that our strategy for using “proteolytic signatures” as a stratification tool will advance the identification
and monitoring of disease as well as aid in biomarker discovery.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Physical Sciences Poster #4
Sampling heterogeneity in tissues
Satwik Rajaram1, Jayant Avva2, Kathy M. Bonness2, Agnieszka K. Witkiewicz3, James S. Malter3, Chloe
E. Atreya4, Lani F. Wu1,2, Steven J. Altschuler1,2
Author Affiliations:
1 Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco,
California, USA
2 Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas,
USA
3 Department of Pathology, University of Texas Southwestern Medical Center, Texas, USA
4 University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, San
Francisco, California, USA
Presenting Author:
Rajaram Satwik
Department of Pharmaceutical Chemistry
University of California at San Francisco
[email protected]
Abstract
Cellular heterogeneity is readily observed in normal and diseased tissues. It is increasingly recognized
that the ability to quantify and compare properties of tissue heterogeneity will play a crucial role in
identifying clinically actionable parameters. How much sub-sampled tissue is sufficient to reliably
represent this heterogeneity? Here, we describe an analytical framework to address this question for
microscopy images, stained using both immunofluorescence and immunohistochemistry. We
demonstrate how our framework can determine the number of Tissue Microarray samples required to
be confident that whole tissue heterogeneity has been captured. Surprisingly, we show that a specified
“tolerance” for allowable difference in heterogeneity can be specified instead by differences in familiar
population-averaged measures, such as mean or percentage of positive pixels. Our approach will
enable rational design of screens to identify functional components of cellular heterogeneity for different
biomarkers, tissue types and diseases.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Physical Sciences Poster #5
ECM Stiffness Enhances Integrin Signaling to Alter Tumor Cell Metabolism
Luke Cassereau, Janna K Mouw, Jonathan Lakins, and Valerie M Weaver
Author Affiliation:
UCSF
Presenting Author:
Luke Cassereau
Surgery
Valerie Weaver
[email protected]
Abstract
Tumors exhibit altered cellular metabolism supportive of continuous cell growth. Nevertheless, the
fundamental molecular mechanisms through which altered metabolism regulate tumor behavior remain
unclear. We previously demonstrated that elevated ECM stiffness and epithelial cell tension drive
squamous carcinoma and mammary transformation, identifying integrin signaling as a key conduit of
ECM mechanical cues and a potent regulator of pro-tumorigenic signaling. We hypothesized that
elevated ECM stiffness potentiates cell metabolism by increasing the expression and activity of key
metabolic targets driven by enhanced pro-tumorigenic signaling via integrin activity to regulate
malignant progression. To test this hypothesis, we profiled metabolic markers using a combination of
H1 NMR, quantitative RT-PCR, immunoblotting and immunofluorescence of MMTV-PyMT transgenic
tumors (± ECM crosslinking) and breast tumor mammary epithelial cells grown on tunable hydrogel
substrates in vitro. To determine the role of integrin signaling, we inhibited integrin signaling used small
molecule inhibitors and, conversely, facilitated integrin signaling through ectopic expression of a β1
integrin clustering construct. We used pharmacological inhibitors targeting glucose uptake, glycolysis,
lactate transport, or oxidative phosphorylation to assess the interplay between ECM stiffness,
metabolism and tumor cell behavior, including invasion, migration, and proliferation. Our data suggests
that ECM stiffening induced elevated tumor cell glycolysis downstream of integrin signaling by targeting
key regulators of glycolysis such as the glucose and lactate transporters and lactate dehydrogenase.
Additionally, inhibitors of metabolism abrogated tumor cell proliferation and invasion in vitro and in vivo.
These data suggest that elevated ECM stiffness drives tumor progression through modulation of tumor
cell metabolism. Additional studies are underway to further clarify how ECM-driven metabolic
dysregulation drives tumor behavior.
Work supported by: NIH F31CA183255 and the ARCS Foundation to LC, NIH R01 CA138818, DoD
W81XWH-13-1-0216, NIH U01ES019458, and NIH R01 CA085492 to VW.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Physical Sciences Poster #6
What’s Your Number?: Using Multimedia Tools to Translate & Disseminate Research Findings
Alexandra N. Anderson , Janice Barlow, Valerie Weaver, Zena Werb, Irene Acerbi, Susan Samson
Presenting Author:
Janice Barlow
Zero Breast Cancer
[email protected]
Abstract
Background: The Breast Cancer and the Environment Research Program (BCERP) supports a
multidisciplinary network of scientists, clinicians, and community partners to examine the effects of
environmental exposures that may predispose a woman to breast cancer throughout her life through
both laboratory and population-based research. The Program includes a basic science project that
studies mammary cells in normal and cancer-prone mice and human cell lines which are used to
understand how environmental factors regulate cell behavior during development and conversion to
cancer. Knowledge of basic science facts and concepts allows for more informed participation by the
community and provides invaluable critical thinking skills to help people make well-informed choices.
Several states, most recently California, have passed laws requiring health providers to inform women
if their mammogram results suggests they have dense breasts and informs them that this is associated
with a higher risk of breast cancer. Although one of the strongest risk factors for breast cancer, breast
density it is not well understood.
Objectives:
1.
To increase awareness of the importance of basic research focused on breast biology, breast
cell communication, and how they influence breast density and breast cancer development.
2.
To develop an educational tool to facilitate a greater understanding of breast biology, what
breast density is, and how breast density might affect future breast cancer risk.
Methods: Working with an animator, the researchers and COTC developed a storyline to accompany
original visuals created for this project. The 17-minute video is and incorporates time-lapse imaging.
The COTC has also received supplemental funds to develop a narrative comic book, available in
English and Spanish that is made up of artwork from the video and brief descriptive prose to
accompany the visuals and ensure that the information is accessible to a variety of learning styles and
reaches a broad audience.
Evaluation: Outreach and dissemination for “What’s Your Number?” will be monitored using metrics
from various channels including social media platforms; UCTV, Vimeo, and YouTube views; and print
distribution. A summative evaluation will also be conducted to determine utilization, effectiveness, and
knowledge gains with health professionals in the individuals who use them.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #1
We Go for Good - Circle the Bay for Breast Cancer
Lamorna Brown Swigart and Malinda Walker
Author Affiliation:
UCSF
Presenting Author:
Lamorna Swigart
Laboratory Medicine
Applied Genomics Laboratory
[email protected]
Abstract
Lamorna and Malinda work within the University of California San Francisco Breast Oncology Program.
In May 2014 Lamorna and Malinda conceived a project to promote exercise and raise awareness of
diseases while supporting charitable causes and having fun. Their initial goal is to ElliptiGO around the
Bay and raise money for breast cancer research programs at UCSF. In the process they seek to draw
attention to the benefits of exercise for reducing the risk of diseases such as breast cancer, diabetes
and many others.
The 230 mile “Circle the Bay” ride is scheduled for June 4-11, 2015. The planned route for “Circle the
Bay” starts in San Francisco then goes south to San Jose, up through Pleasanton and Livermore, and
north to Napa, then west through Sonoma to Petaluma, and finally south back to San Francisco.
The funds raised will go to support UCSF Breast Cancer programs such as the Athena Breast Health
Network, the I-SPY2 breast cancer trial, and seed funding for developing novel breast cancer research
projects at UCSF. They have a fund raising target of $100,000.
As Lamorna and Malinda “Circle the Bay” on ElliptiGO they will be holding events at their midday and
evening stops, which will give them and opportunity share with the audience about I-SPY 2, the Athena
Breast Health Network and other breast cancer research projects at UCSF.
Here we illustrate the route, list our rest/event stops and challenge our audience to get involved and
support us along the way.
Thank you for following, or joining, us on our journey.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #2
The I-SPY 2 TRIAL: Serial sample collection for biomarker studies and early identification of
non-reponders.
Lamorna Brown Swigart, Pat Glenn, Aye Aye Ma, Licia Dean, Kim Etzel, Luana Griffin, Vidya
Sheshadri, Both Dargis, Carissa Santos, Alfred Au, Ron Balassanian, Yun-Yi Chen, Gregor Krings,
Laura Esserman and Laura van 't Veer
Presenting Author:
Lamorna Swigart
Laboratory Medicine
Applied Genomics Laboratory - I-SPY 2 TRIAL
[email protected]
Abstract
The I-SPY 2 TRIAL is an adaptive neoadjuvant trial for women with newly diagnosed, locally advanced
breast cancer. The trail is enrolling patients at approximately 20 centers across North America. The trial
design includes a master Investigational New Drug FDA approval that allows multiple novel drugs to be
tested in the trial. Patients who consent and meet inclusion criteria receive standard of care treatment
with or without one of the novel agents. The goal of the trail is to identify drug regimens that have ≥
85% predictive probability of success in a neoadjuvant 300-patient phase 3 trial of patients in any of 10
possible signatures defined by HR, HER2, and MammaPrint. The adaptive aspect of the trial is
achieved through a randomization engine that learns, from patients that have completed therapy, which
signatures respond best to a given drug. The randomization engine then alters the odds of assignment
to that arm accordingly. A secondary aim of the trial is to identify companion biomarkers that can be
used to select patients who would benefit from the novel drug.
Women who consent to screening undergo biopsies to provide material for MammaPrint and provide
further biopsies three weeks after the start of treatment and at the time of surgery. These, and
concurrent blood samples, are sent to the central I-SPY lab at UCSF. The longitudinal collection of
samples allows evaluation of changes within the tumor under the influence of the drug combinations.
Such changes may be indicative of a pathological response that will result in reduction of cancer
burden. Conversely change, or the absence of change, may be an early indication of failure to respond.
This knowledge may be used to adapt treatment for a non-responding patient earlier in her treatment.
Here we describe the samples collected and the methods used to ensure pathological quality in
material used for biomarker assays.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #3
Developing silastic tubing for local delivery of hormonal therapy: a novel approach to breast
cancer prevention
Jeenah Park1, Merisa Piper2, Scott Thomas3, Pamela N. Munster4
Author Affiliations:
1 UCSF Division of Hematology and Oncology, Dept of Medicine
2 UCSF Dept of Surgery
3 UCSF Division of Hematology and Oncology, Dept of Medicine
4 UCSF Division of Hematology and Oncology, Dept of Medicine
Presenting Author:
Jeenah Park
Division of Hematology and Oncology, Dept of Medicine
[email protected]
Abstract
Breast cancer remains a considerable public health burden. Current use of systemic use of antiestrogens is associated with undesirable side effects and poor bioavailability in young women. Surgical
removal of the breasts is unacceptable to most women, even for those known to be at high risk for
breast cancer. As such, many high risk women opt for neither measure, thus highlighting the need for
prevention alternatives.
Our preliminary data suggest that silastic tubing is capable of acting as a fulvestrant depot and could be
used to delivery fulvestrant selectively to the breast tissue. After the tubing was loaded with dry
fulvestrant and placed in tissue culture media for increasing times up to 30 days, fulvestrant released
from the tubing for 5 days was sufficient to achieve growth inhibition in MCF7 ER+ breast cancer cells
comparable to that of cells directly treated with clinical concentration of fulvestrant (100 nM). To
simulate human physiology in which drugs are washed out in the body, tubing-containing media was
harvested everyday or every 3.5 days for 12 weeks and replenished with fresh media. Repeat washout
experiments revealed that drug release is constant over each washout period. It further demonstrated
that fulvestrant released from the tubing can down-regulate ER, PR, and cyclin D1 expression and
induce growth arrest in MCF7 and T47D cells. Fulvestrant release from silastic tubing was quantified by
an LC-MS/MS method, at day 15 and 30. Fulvestrant levels were 130 nM and 260 nM, respectively,
substantially exceeding required plasma levels for breast cancer treatment.
Our data suggest that silastic tubing may act as a novel depot for local delivery of anti-estrogens to the
breast. Future studies include characterization of the fulvestrant release in in vivo mouse models,
comparison of fulvestrant uptake by mammary tissue vs blood, and analysis of its efficacy in preventing
orthotopic tumor formation. Our study will provide the scientific basis for translating this novel breast
cancer preventive approach to the clinic.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #4
Targeting Urokinase Receptor for Diagnosis and Therapy of Aggressive Breast Cancers
Efrat Harel1, Samantha Liang1, Zev Gartne1, Laura van 't Veer2, Charles Craik1
Author Affiliations:
1 Department of Pharmaceutical Chemistry, UCSF
2 Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, UCSF
Presenting Author:
Efrat Harel
Department of Pharmaceutical Chemistry
Charles Craik
[email protected]
Abstract
Triple negative breast cancer (TNBC) is an aggressive subtype of BC associated with poor prognosis,
worse overall survival and earlier recurrence. Targeted therapies such as epidermal growth factor
receptor inhibitors, showed variable response rates but no survival benefit. One hallmark of aggressive
cancers is increased urokinase receptor (uPAR) expression. As a heavily glycosylated, GPI linked
protein, its ubiquitousness in many aggressive cancer types–TNBC in particular–makes it an attractive
target for uPAR-directed therapies. uPAR participates in many protein/protein interactions, which leads
to pericellular proteolysis and “outside-in” signaling that is mediated by specific integrins. Therefore,
inhibition of one or more of these interactions would progressively contribute to a reduction in
aggressive behavior.
We identified 6 inhibitory anti-uPAR Antibodies. Two of those antibodies, referred to as 2G10 and 3C6,
obstruct protein-protein interactions between uPAR and uPA or b1 integrin, respectively. The antibodies
were tested in in vitro and in vivo TNBC models and showed diagnostic and therapeutic potential. In a
mouse model of TNBC the antibodies targeting two distinct subdomains of slowed or blocked tumor
growth. Moreover, treatment of TNBC cell lines in vitro with a combination of 2G10 and 3C6
demonstrated synergy, suggesting that blocking multiple uPAR effector functions simultaneously may
provide a dramatically enhanced response.
The anti uPAR Antibodies have been assembled using a modular platform to give bi-specific antibodies
based on DNA linkers. The platform enables a library of heterofunctional molecules to be made with
precise geometries, valencies, and rigidities. Basic linear construct combining 3C6 and 2G10, have
been tested for uPAR recognition ability and therapeutic effect in vitro in TNBC cell lines. Our results
indicate that at fixed total protein concentration, the scaffolded antibodies outperform the unscaffolded
antibodies in blocking MDA-MD-231 cell invasion.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #5
Preclinical testing of PARP inhibition in breast cancer cell lines
Saima Hassan, Amanda Esch, Koei Chin, Laura Heiser, Joe W. Gray
Author Affiliation:
Department of Biomedical Engineering, Oregon Health and Science University
Presenting Author:
Saima Hassan
Oregon Health and Science University
Gray Lab
[email protected]
Abstract
Background: PARP (Poly-ADP ribose polymerase) inhibitors are targeted therapeutic agents that inhibit
the activity of the PARP enzyme and block the repair of DNA breaks. PARP inhibitors have been found
to be more effective in those patients with an increased inherited risk of developing breast, with
mutations in the BRCA1/2 genes. Although several clinical trials have demonstrated efficacy of PARP
inhibitors in breast cancer patients, it is not well understood which patients will most benefit from this
therapy. In order to better understand the breast cancer subtypes that will respond best to anti-PARP
therapy from the laboratory, our first objective is to identify indicators of therapeutic response in a panel
of breast cancer cell lines.
Methods: Cells were seeded in 384-well plates, and PARP inhibitors were administered 24 hours postseeding. Nine concentrations of each therapeutic agent (veliparib and BMN 673) were tested in a
panel of 9 breast cancer cell lines. After 6 days, cells were imaged using wide-field microscopy
(Scan^R, Olympus). Endpoints examined were cell count and expression of DNA damage response
protein, 53BP1 (p53 binding protein-1). Cell counts were used to calculate IC50 values and 53BP1
foci count per cell were used to calculate a fold-induction ratio in treated versus untreated cells.
Results: Across 9 breast cancer cell lines, mean IC50 value for veliparib was 40.2 μM (range, 2.7 115.2 μM), and for BMN 673 was 34.2 nM (range, 2.4 – 92.4 nM). The rank list of most sensitive to
resistant cell line was different for each therapeutic agent, however both therapeutic agents were
effective in both BRCA1/2 mutant and wildtype breast cancer cell lines. The mean fold-induction of
53BP1 foci across 7 breast cancer cell lines was 2.2 (range, 1.5 – 3.2) for veliparib, and 2.7 (range, 1 –
5.5) for BMN 673.
Conclusions: Efficacy of veliparib and BMN 673 were identified in BRCA1/2 mutated and BRCA1/2
wildtype breast cancer cell lines. BMN 673 is more potent than veliparib, with a therapeutic response
obtained in nanomolar concentrations, as opposed to micromolar concentrations. 53BP1 expression
modulates with increasing concentrations of PARP inhibition.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #6
Potential impact of veliparib tumor concentrations and typical non-adherence in triple negative
breast cancer on treatment efficacy, a simulation study
Imke H. Bartelink1, Ron Keizer1, Denise Wolf2,Weiming Ruan2, Brendan Prideaux4, Pei Rong Evelyn
Lee2, Jean-Philippe Coppé2, Gregor Krings5, Lisa Wilmes6, Byron Hann3, Lamorna Brown Swigart2,
Laura Esserman2, Alan Wu2, Laura van ’t Veer2, Rada Savic1
Author Affiliations:
1 Bioengineering & Therapeutic Sciences of the University of California San Francisco, CA
2 Laboratory Medicine, UCSF Helen Diller Family Comprehensive of the University of California San
Francisco, CA
3 Preclinical Therapeutics Core, UCSF Helen Diller Family Comprehensive Cancer Center of the
University of California San Francisco, CA
4 Mass Spectrometry Imaging Laboratory, New Jersey Medical School Public Health Research Institute
Rutgers, The State University of New Jersey, Newark
5 Department of Pathology of the University of California San Francisco, CA
6 Department of Radiology of the University of California San Francisco, CA
Presenting Author:
Imke Bartelink
B&TS
van 't Veer lab
[email protected]
Abstract
Background: Although Veliparib + carboplatin has shown significant efficacy in triple negative breast
cancer (TNBC) patients, 42% of veliparib-treated TNBC patients in I-SPY 2 did not optimally respond.
We hypothesize that insufficient veliparib tumor concentrations lead to inadequate response in some
TNBC patients. We aim to evaluate the impact of adherence on tumor drug exposure and the potential
impact of tumor veliparib concentrations on efficacy.
Methods: 30 MDA.MB.231, HCC70 or MDA.MB.436 mammary fat pad-implanted mice received
carboplatin + veliparib 20mg/kg or 60mg/kg three times daily for three days via oral gavage. Sparsely
sampled plasma and tumor concentrations and previously published time-concentration profiles 1200mg/kg dosed SCID-mice were analyzed using nonlinear mixed-effects modeling. Scaling to humans
occurred by linking the mouse tumor model to previously published plasma pharmacokinetic model in
patients. This linked model was used to simulate tumor concentrations in patients at full adherence and
published typical 82% adherence. The results were compared with previously published In vitro derived
IC50 for veliparib + carboplatin in (non-TNBC) cells: BRCA1: IC50=0.15 μmol/L, BRCA2: IC50=0.04
μmol/Land wildtype: IC50=5-50 μmol/L. The threshold for adequate response in patients was set at
having a concentration above these IC50 values over 10% of the treatment duration.
Results: Three hours after administration, veliparib concentrations in mouse tumors were significantly
lower than in plasma (P=0.001). Drug penetration was not significantly different between mouse tumors
derived from the three different TNBC cell lines. Veliparib displayed non-linear plasma clearance
(P<0.001 vs linear clearance). Tumor penetration was saturated at the 60mg/kg dose (P <0.001).
Clinical trial simulations of veliparib 50mg twice daily dose predicted that only BRCA mutation carriers
reached the threshold for adequate response. 100% reached this threshold at full adherence, whereas
at typical adherence, 80% of BRCA1 and 83% BRCA2 carriers exceeded the threshold. The threshold
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
for adequate response was not reached in any of BRCA wild type patient simulations (n=1000), even at
100% adherence.
Conclusions: Simulations combining preliminary in vitro, mice and patient data suggest that the dose
needed in BRCA mutation carriers could be less than non-carriers.With typical adherence, the dosing
as used in I-SPY 2 patients may not be sufficient for patients with BRCA mutations or wildtype TNBC.
Measurements of adherence and tumor concentrations associated with outcomes in patients may
confirm these predictions.
Figure: simulated concentrations in plasma and TNBC in patients after 50mg twice daily dosing of
veliparib and the minimal effective concentration derived from BRCA1/2/wildtype cells.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #7
Optimization of Magnetic Resonance Imaging Predictive Performance by Breast Cancer Subtype
for Predicting Response to Neoadjuvant Chemotherapy
Wen Li1, Wei-Ching Lo1, Ella Jones1, David Newitt1, John Kornak2, Lisa Wilmes1, Laura Esserman3,
Nola Hylton1
Author Affiliations:
1 Radiology & Biomedical Imaging
2 Epidemiology and Biostatistics
3 Surgery and Radiology
Presenting Author:
Wen Li
Radiology and Biomedical Imaging
Breast MRI
[email protected]
Abstract
The purpose of this study is to optimize the predictive performance of functional tumor volume (FTV)
computed from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). In this
retrospective study, we investigate the association of FTV influenced by PEt and SERt values with
recurrence-free survival (RFS) in breast cancer subtypes defined by hormone receptor (HR) and HER2
status. 64 patients with locally advanced breast cancer were imaged by DCE-MRI before treatment
(MRI1), after one cycle of adriamycin-cytoxan (AC) therapy (MRI2), inter-regimen (MRI3, taxane
receivers only) and at the completion of chemotherapy prior to surgery (MRI4). Because treatment
length and regimen varied among patients, the MRI exam performed after all NACT and before surgery
was designated as final MRI (MRIf). FTV was calculated with varying PEt (30–200% in steps of 10%)
and SERt (0–2 in steps of 0.2) values. A Cox proportional hazard model was used to analyze
association with RFS, defined as the time between surgery and disease recurrence or last disease-free
follow-up, for the following imaging predictors: early percent change in FTV (ΔFTV2: MRI1 vs. MRI2),
final percent change (ΔFTVf: MRI1 vs. MRIf), and final FTV (FTVf). RFS association was evaluated for
the full cohort and within subsets defined by tumor subtype (HR+/HER2-, HER2+, triple negative).
Estimated hazard ratios per unit change in predictors, associated 95% confidence intervals (CI) and pvalues were evaluated. The cutoff of p<0.05 was used to differentiate PEt/SERt values with higher
predictive performance. The peak hazard ratios in the full cohort were located in different PEt/SERt
combinations for different predictors and none of them occurred at the empirical setting – 70%/0. When
analyzed by tumor subtypes, different prediction profiles were observed. While this study is
retrospective in nature and had small sample size, the findings nevertheless suggest that performance
of imaging predictors based on FTV may be improved if threshold optimization is performed separately
for the clinically-relevant subtypes defined by HR and HER2 receptor expression.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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2015 UCSF Breast Oncology Program Scientific Retreat
Therapeutics and Clinical Trials Poster #8
A Systems Approach Combining Genomics, Advocacy, and Emerging Therapeutics to Address
Triple-Negative Breast Cancer (TNBC) Outcome Disparities
Alicia Y. Zhou1*, Maria Martins1*, Alexandra Corella1, Dai Horiuchi1, Christina Yau1, Taha
Rakshandehroo1, John Gordan1, Rebecca Levin1, Jeff Johnson1, John Jascur1, Mike Shales1, Antonio
Sorrentino1, Jaime Cheah2, Paul Clemens2, Alykhan Shamji2, Stuart Schreiber2,3, Nevan Krogan1,
Kevan Shokat1,3, Susan Samson1, Frank McCormick1, Andrei Goga1, Sourav Bandyopadhyay2
Author Affiliations:
1 University of California San Francisco
2 The Broad Institute of Harvard and MIT
3 Howard Hughes Medical Institute
Presenting Author:
Alicia Zhou
Cell and Tissue Biology
Susan Samson
Breast Science Advocate
Goga Lab
[email protected]
Abstract
There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can
be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions
or emergent dependencies that cancer cells acquire in the presence of specific mutations. Using
engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map
that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly
predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model
more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable
interactions with the MYC oncogene including resistance to AKT/PI3K pathway inhibitors and an
unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner, providing new
drug and biomarker pairs for clinical investigation. This scalable approach enables the prediction of
drug responses from patient data and can be used to accelerate the development of new genotypedirected therapies.
This retreat is supported in part by Nektar Therapeutics, a conference award from the California Breast Cancer Research Program
(21MB-0004), Celgene Corporation, Puma Biotechnology, and the UCSF Helen Diller Family Comprehensive Cancer Center
Support Grant (P30 CA082103).
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