Breast Cancer Research Program

Seattle Cancer Consortium Breast SPORE

Seattle Cancer Consortium Breast SPORE

Principal Investigators:        Peggy L. Porter, MD
                                            Martin “Mac” Cheever, MD

Overall Program Description
The Seattle Cancer Consortium (SCC) Breast SPORE application, led by Drs. Peggy Porter and Martin
“Mac” Cheever, brings together clinical and laboratory researchers from the Fred Hutchinson Cancer
Research Center (FHCRC) and the University of Washington (UW) with a goal to positively impact breast
cancer prevention, detection, treatment and care of women who have, or are at risk for, the disease. To
achieve that goal, we will carry out strategic research in highly translational projects, develop new research directions as the SPORE progresses, and sponsor new investigators—those starting their careers and those with established careers newly focusing on breast cancer.

The investigators in this SPORE view the highly variable response of breast cancers to current therapies as a manifestation of the genotypic and phenotypic heterogeneity of the disease. Therefore, the initial projects on the SPORE will focus on the supposition that targeted treatments need to be focused on the appropriate tumor type. The four major research projects proposed for the Seattle SPORE expand on this theme. Two of the projects are initiated with clinical trials and a focused bed-side-to-bench translational approach. Three of the projects are focused on gaining insight into resistance to therapy and eventually defining what targeted therapies are needed to treat resistant tumors. Project 1 will apply basic discovery of p27kip1 cell cycle regulation in breast cancer to predict mortality and response to therapy. Project 2 will use exquisitely specific and engineered central memory T cells to target abnormally expressed tumor-associated proteins with vaccines and therapy. Project 3 will determine the biological basis for a breast imaging metabolism/perfusion mismatch profile that predicts poor prognosis and poor response to systemic therapy. Project 4, will draw on a well-characterized population-based cohort to identify specific DNA damage pathway biomarkers that could prevent the over, or under, treatment of women with breast cancer.

Together, these four projects afford both short- and long-term translational rewards and potential for new discoveries that will impact important aspects of breast cancer care. The SPORE is enhanced by a Developmental Research Program (DRP), a Career Development Program (CDP) and four supporting Cores: Leadership, Specimen Acquisition and Pathology, Clinical, and Biostatistics. These elements, along with the existing highly interactive and interdisciplinary environment and outstanding institutional support for breast cancer research in the FH/UW Cancer Consortium, ensure a successful translational SPORE program in breast cancer.

PROJECT 1: Cytoplasmic mislocalization of p27Kip1 as a causative factor and prognostic marker in human breast cancer

Project Co-Leaders:    James Roberts, MD
                                    Peggy Porter, MD

Co-Investigators:         Julie Gralow, MD
                                    Li Hsu, PhD

Although aggressive tumors often express abnormally low amounts of the cell cycle inhibitor p27Kip1 (p27), this is almost never due to mutation of the p27 gene. Although the data supporting the importance of p27 as a prognostic indicator are strong, it is ultimately the relationship that we and others are defining between p27 and response to specific breast cancer therapies that will expand the clinical utility of this single marker. It is sometimes assumed that p27 is a surrogate for proliferation and that it is not prognostic or predictive beyond its role in inhibiting the cell cycle. In this project, we will build on basic findings that confirm p27 function is more complicated and that its regulation and cellular localization mediate tumor progression and cellular responsiveness to therapies directed at breast cancer cells. We will begin the translation of these basic discoveries by evaluating the relationship between clinical outcome and p27 expression and cellular localization in human breast cancers of women with at least five years of follow-up for breast cancer mortality. Compelling evidence indicates that the cellular localization of p27 could be an indicator of response to two important breast cancer therapies: anti-estrogen and anti-HER2. To characterize the effect of an anti-estrogen and trastuzumab on expression and localization of p27, we will assay protein levels in samples pre- and post-administration of these agents. These relatively small human studies will guide the evaluation of p27 in larger clinical trials that have the power to assess the ability of this protein to predict response to therapy. In parallel we will be investigating a new pathway, involving TRIM62, that may be responsible, at least in part, for the cytoplasmic expression of p27 in HER2+ human breast cancers. We propose three aims: Aim 1 will test the hypothesis that cytoplasmic p27 is a breast cancer oncogene affecting tumor initiation, invasion and metastasis. Aim 2 will test the hypothesis that regulation of p27 by TRIM62, a new p27 regulator, plays an essential role in HER2-dependent oncogenic transformation. Aim 3 will further test the hypothesis that increased cytoplasmic p27 is a prognostic marker in human breast cancer, and ask whether cytoplasmic p27 predicts responsiveness to specific breast cancer therapeutics.

Loss of p27 in tumor cells has been shown to be a marker of poor outcome for breast cancer. This project will test the possibility that cytoplasmic p27 expression predicts poor prognosis or response to anti-estrogen and/or anti-HER2 therapies. If it does, it will be possible to develop a method and assay that will not only be able to predict who will fail treatment, but will also allow us and others to gain insight into what targeted therapies are needed to treat resistant tumors.

PROJECT 2: Targeted immunotherapy of breast cancer with central memory T cells

Project Co-Leaders:     Stanley Riddell, MD
                                    Lupe Salazar, MD

Co-Investigators:         Vijayakrishna K. Gadi, MD, PhD
                                    Shelly Heimfeld, PhD
                                    Ted Gooley, PhD

The translational goal of this project is to evaluate the adoptive transfer of tumor-specific T cells derived or engineered from central memory cells to treat breast cancer. The immune system is designed to distinguish diseased from normal cells with exquisite specificity and sensitivity, and there is increasing evidence that tumor development and progression is restrained by adaptive host T cell responses to tumor-associated antigens. However, harnessing this activity to provide therapeutic benefit in breast cancer requires identifying antigens that are expressed by tumor cells and can be safely targeted, and developing methods to achieve potent and durable T cell immunity in patients. Many candidate tumor associated antigens have been discovered in breast cancer and we have focused on targeting the HER-2 oncoprotein and NY-BR-1. We have pursued the adoptive transfer of T cells specific for these antigens because this approach should allow for control of the specificity, function, and magnitude of the antitumor response, and could overcome obstacles that limit the endogenous host response, or T cell responses elicited by vaccination. The efficacy of adoptive T cell therapy in clinical trials for other human malignancies has been limited by the inability of tumor-specific effector cells that have been expanded in vitro to persist at high levels in vivo after adoptive transfer. Studies in our lab have demonstrated that the survival of adoptively transferred T cells is correlated with the differentiation state of the precursor T cell from which the T cells are derived. Effector cells isolated from central memory but not effector memory T cells provide persistent engraftment, migrate to memory T cell niches, function in vivo after adoptive transfer, and can be sustained at remarkably high levels by a short course of IL-15. This project will build on these findings and evaluate the adoptive transfer of T cells derived or engineered from central memory cells to treat breast cancer. The specific aims are: 1. To perform a phase I trial of adoptive T cell therapy with TCM-derived HER-2/neu (HER-2)-specific T cells following in vivo priming with a HER-2 peptide vaccine in patients with advanced HER-2+ breast cancer. 2. To engineer CD45RO+ CD62L+ TCM derived effector T cells through T cell receptor (TCR) gene transfer to express a TCR that targets NY-BR-1. 3. To perform a phase I study of adoptive T cell therapy with TCR modified TCM to target NY-BR-1 in patients with advanced NY-BR-1+ breast cancer.

There is evidence breast cancer is detected by the immune system, but the development of immunotherapy that improves the outcome for patients has been challenging. The proposed studies will evaluate new approaches to the immunotherapy for breast cancer in which cells of the immune system that have the capacity to survive long term, will be isolated, programmed to target and kill tumor cells and transferred back to the patient. The results of these studies will provide insights into the potential utility of adoptive T cell therapy for breast cancer, and for the broader application of this approach in human malignancy.

PROJECT 3: Metabolic Alterations in Advanced Breast Cancer and Response to Systemic Therapy

Project Co-Leaders:     David Hockenbery, MD
                                    Jennifer Specht, MD

Co-Investigators:         Janet Eary, MD
                                    Lara Gamble, PhD
                                    Li Hsu, PhD
                                    Constance Lehman, MD, PhD
                                    Fionnuala Morrish, PhD
                                    Savannah Partridge, PhD
                                    Andrew Shields, MD
                                    Barry Storer, PhD

The use of systemic chemotherapy for breast cancer has contributed to the recent decline in breast cancer mortality; however, an unacceptable number of patients fail systemic therapy and die of disseminated disease. Identifying factors important in resistance and directing patients towards more effective treatment is the translational goal of Project 3. Using quantitative PET imaging to measure glucose metabolism, and more recently dynamic contrast-enhanced (DCE) MRI to measure blood flow, we have identified an in vivo metabolic signature for locally advanced breast cancer (LABC) resistant to neoadjuvant chemotherapy as (1) a pre-therapy mismatch between metabolism and perfusion, (2) persistent or even increased tumor perfusion despite treatment, and (3) an altered pattern of glucose metabolism relative to glucose delivery after treatment. This pattern predicts incomplete response, early relapse and death independent of established prognostic factors, including pathologic primary tumor and nodal pathologic response. We have also found this pattern is more profoundly associated with triple-negative (TN, ER/PR/HER2 negative) tumors versus those that express ER/PR and/or over-express HER2.

We now propose to translate our clinical, in vivo findings in patients back into the laboratory to identify the biologic features of tumors underlying these findings. In a cohort of LABC patients undergoing neoadjuvant chemotherapy, we will (1) compare imaging findings to tumor phenotype determined by IHC and expression microarrays to determine which molecular pathways are most involved in the resistant imaging phenotype, (2) determine the role of the tumor microenvironment, specifically tumor hypoxia measured by FMISO PET and the expression of the hypoxic tissue markers measured by IHC, and (3) relate macroscopic metabolic properties measured by imaging to cellular metabolism in biopsy specimens and a panel of cell lines using ToF-SIMS, with the goal of relating findings on metabolic pathways measured in cell lines to the resistant phenotype seen in patients. Successful completion of the studies will identify breast cancer patients likely to fail systemic chemotherapy and direct therapy towards those biologic targets most likely to overcome resistance.

This Project will investigate quantitative in vivo imaging as a means of identifying breast cancers resistant to systemic therapy and directing the patient towards more effective therapy. The primary translational goal of the project is to relate in vivo imaging findings predictive of poor response and patient outcome to underlying tumor biology with the goal of directing treatment targeted to specific resistance factors.

PROJECT 4: Population-based study of DNA damage response markers of prognosis in breast cancer

Project Co-Leaders:       Amanda Paulovich, MD, PhD
                                       Kathleen Malone, PhD

Co-Investigators:            Pei Wang, PhD

The translational goal of Project 4 is to identify markers of the DNA damage response (DDR) pathway that will improve our ability to predict outcome in breast cancer and prevent the over, or under, treatment of disease. Our foundation for evaluating candidate markers of outcome is a population-based cohort of 2337 women (approximately 1900 with available tumors) ages 45-79 diagnosed with invasive breast cancer who are being followed for recurrence and death (QUILT Study). This well-characterized cohort, which was specifically designed to assess determinants of recurrence and mortality, offers unique benefits in elucidating insights into outcomes, including: comprehensive pre- and post-diagnostic exposure data, complete treatment and medical history data, flexibility and efficiency in examining different hypotheses, information on and ability to control for many different potential confounders, and inclusion of a broad spectrum of cases.

Breast cancer morbidity and mortality is substantial and there is an acute need for additional tumor markers (beyond histopathology, ER and Her2) that can predict outcome, serve as therapeutic targets, and/or guide therapy in newly diagnosed patients. Compelling evidence, largely centered on p53, indicates that the DDR pathway is a promising (but understudied) source of clinical prognostic and predictive markers for breast cancer. The lack of a clinically tractable assay to assess DDR activity has inhibited investigations to date and also, because DDR involves both p53-dependent and p53–independent responses, p53 status alone is an insufficient measure of activity or functionality of the signal transduction cascade.

We will conduct a comprehensive assessment of the DDR pathway activity in human breast cancers via a multi-analyte marker panel designed to capture DDR pathway function. We will assess the association of
DDR activity with breast cancer prognosis and treatment response, using the population-based cohort described above. Our specific aims are: (1) Using the QUILT Study population-based cohort and DDR markers identified from the literature and from discovery in Aim 2, test whether activation of the DNA damage response is predictive or prognostic in breast cancer; (2) Identify proteins and transcripts elevated upon activation of the DNA damage response in human mammary epithelial cells (ex vivo), and determine which of the responsive proteins are detectable in human breast cancer tissues.

This project will investigate markers of DNA damage repair (DDR) pathway activity for their potential to predict future recurrence and death from breast cancer and to improve treatment decision-making.
Candidate DDR markers will be tested for their relationship with recurrence and mortality in a well-characterized population-based cohort study of women with invasive breast cancer who are being followed for survival.

Core A: Leadership

Core Co-Directors:       Peggy L. Porter, MD
                                     Martin (Mac) Cheever, MD

The Leadership Core provides the overall context for the translational activities of the SPORE and builds on established interdisciplinary collaborations. Dr. Porter and Dr. Cheever, Co-PIs of the SPORE, will co-direct the Core and lead an Executive Committee (EC), composed of all Project and Core leaders and breast cancer patient advocates, primarily responsible for overall planning and evaluation. The EC will be advised on scientific direction, planning and evaluation of the translational progress of SPORE projects and activities by both an External Advisory Board (EAB), which includes three national SPORE leaders, and an Internal Advisory Board (IAB), which include two SPORE leaders. To maintain a high degree of translational research focus to all SPORE activities, the EC will meet and interact regularly with the SPORE Career Development Program (CDP) and Developmental Research Program (DRP) committees, and the SPORE Statistical Working Group (SWG).

The aims of the Administrative Core are to:
1. Provide oversight of all SPORE activities to meet the scientific and administrative needs of the individual research projects and cores
2. In consultation with EAB members, integrate new projects into the SPORE
3. Provide an organizational structure within the FHCRC/UW Cancer Consortium (Consortium), which
a. promotes interaction between interdisciplinary investigators, in and outside of the SPORE
b. evaluates progress towards translational goals
c. encourages, selects and guides new research and developmental projects
d. provides career mentorship and entry of women and minorities into the field of breast cancer research
4. Promote SPORE-SPORE interactions, within and outside the Consortium
5. Provide fiscal management of grant funds and records in compliance with all regulations and requirements, including Radiation Safety, Animal Care, and Protection of Human Subjects
6. Communicate and consult with NCI project officers

CORE B: Specimen Acquisition and Pathology

Core Director:       Peggy Porter, MD

Co-investigator:     Ming-Gang Lin, MD

The Specimen Acquisition and Pathology Core is a key component of the SPORE and will support the translational goals of SPORE Projects, as well as developmental projects funded through the SPORE. Dr.
Porter’s leadership will provide not only research and clinical breast pathology expertise but also integration of Core B activities with the SPORE overall, and developmental projects in particular. This coordination of specimen acquisition and distribution with promotion of new research will greatly aid translation of basic discoveries into experiments involving human samples. The Core augments the existing robust FHCRC/UW Cancer Consortium Breast Specimen Repository and Registry (BSRR) and will function to centralize specimen acquisition, processing, pathologic analysis and distribution of samples needed by SPORE projects. It will also provide a laboratory base for select biomarker assays in support of the major and developmental projects.

Specifically the Core will:
1. Use the established and efficient BSRR to procure and distribute tissue and blood specimens for
2. SPORE and developmental projects
3. Perform protocol-specific specimen processing for SPORE and developmental projects
4. Maintain a database that allows specimen tracking and distribution, linkage with relevant deidentified data, and data sharing with other projects and cores
5. Provide high-quality pathology support for SPORE and developmental projects including:
• Pathology review of tissues at various levels of complexity
• Histology sectioning and preparation of section slides for histologic evaluation
• Immunohistochemistry (IHC), and new antibody work-up and optimization
• IHC interpretation of both immunoperoxidase and immunofluorescence stains
• Laser capture microdissection (LCM)
• Tissue microarray (TMA) design, construction, sectioning, and imaging

The Specimen Acquisition and Pathology Core is a key component of the SPORE and will support the translational goals of the projects and developmental projects. The core will take full advantage of institutional resources, integrate them for efficient use by SPORE investigators, and flexibly adapt to needs and new developmental projects during the time frame of the SPORE grant.

CORE C: Clinical

Core Director:    Julie Gralow, MD

Co-investigators: Vijayakrishna K. Gadi, MD, PhD
                            Jennifer Specht, MD

For translational research to be successful there must be a two-way flow of information, from the clinic to the laboratory and from laboratory to clinic. Clinical interaction with patients and health care providers is crucial to the success of the research studies proposed within the SPORE, and to the long-term success of a translational program of breast cancer research. The Clinical Core of the SPORE program provides this critical link by incorporating a highly-effective breast cancer clinical team into the overall structure of the SPORE. The Clinical Core will be responsible for facilitating translational research through the support of clinical trials and clinical research studies, as well as providing clinical education throughout the program. Additionally, the Clinical Core will serve to mentor and find clinical collaborators for laboratory investigators, with particular emphasis on those funded through the SPORE’s Developmental Research Program.

The Clinical Core will assist SPORE investigators interested in initiating a clinical study, including preparation, review, approval, and activation of clinical studies. Interactions with patients and health care providers will be initiated and facilitated by the Clinical Core. The Core research manager will supervise research staff who will assist with SPORE-related clinical trials to ensure that accrual is achieved, overseeing clinical trials recruitment efforts, screening for trial eligibility, and contacting potential patients regarding study participation. The Core will communicate with institutional and regional oncology providers to seek physician support for referral into SPORE projects. The Core will consent and follow-up patients appropriate for SPORE projects and provide clinical and outcome data as required by these studies. The Clinical Core staff will be responsible for assuring that the clinical protocol is safely and properly followed, including monitoring toxicities and reporting adverse events. They will provide support and education to participating patients, assist in the administration of therapy, and assure timely entry of clinical data. By design, the Clinical Core will work closely with the Specimen Acquisition and Pathology Core, which will procure and process specimens for SPORE projects after initial contact is made through the Clinical Core. The Clinical Core will interact closely with the Biostatistical Core in designing and analyzing studies, and will be in close interface with the FHCRC/UW Consortium’s Clinical Trials Support Office that is responsible for management of all clinical trials.

The importance of clinical expertise to effectively carry out translational research objectives cannot be overstated. Laboratory discoveries can only be developed into clinical tools if clinical input is incorporated early into all aspects of research planning and implementation. This Core is well-positioned to take advantage of FHCRC/UW Consortium research, clinical strengths and institutional alliances to maximize exchange of ideas and facilitate translation, both to and from the clinic.

CORE D: Biostatistics

Core Director:         Li Hsu, PhD

Co-investigators:    Ted Gooley, PhD
                               Barry Storer, PhD
                               Pei Wang, PhD

The Biostatistics Core will provide essential biostatistical support to Seattle Cancer Consortium Breast
SPORE investigators. The Core links study design, data collection, measurements, and analysis to the critical hypotheses and questions studied by SPORE investigators whose research involves basic sciences, epidemiology, population studies, and clinical research. The Biostatistics Core will contribute to the SPORE mission through the following specific aims:
1. Study design: Define study hypotheses, study populations, and experimental measurements to answer research questions of interest, avoid systematic bias, and ensure a high likelihood of detection of biologically meaningful effects.
2. Analysis and interpretation: Identify and implement appropriate quantitative methods to address scientific questions of interest and provide valid statistical inferences about the evidence supporting the various study hypotheses.
3. Methodological development when needed: Modify existing approaches and develop novel study designs and methods to address problems arising from SPORE projects, where appropriate statistical methods are inadequate.

SPORE biostatisticians have been closely involved with the projects in the SPORE. They will continue to collaborate as co-investigators on each project to ensure that studies are well designed and appropriately analyzed and interpreted. Moreover, the Core will provide consulting services to SPORE investigators for projects under the Research Developmental Program and the Career Development Program. The Core investigators have diverse and complementary expertise, and can conduct analyses using data from a wide variety of experimental technologies. For some of these technologies, analytic methods are still evolving. Core investigators are part of Consortium biostatistical research groups that are leaders in the areas of biomarker development, computational biology, and bioinformatics. In summary, the Core is well equipped to meet the diverse needs and address the translational aims of the Breast SPORE.

This new Core will provide essential statistical support and analysis to current and future SPORE projects.

Developmental Research Program

Director:             Peggy L. Porter, MD

The goal of the Developmental Research Program (DRP) in the Seattle Cancer Consortium (SCC) Breast
SPORE is to identify, fund and nurture innovative projects that have the potential to become outstanding translational research efforts. This will ensure that mature projects are in the pipeline when current projects meet their translational goals or when SPORE Projects fail to meet their aims and need to be replaced. Additionally, it will ensure that mature projects are ready for the competing renewal application towards the end of the grant period.

The members of the SPORE realize that real research progress requires that all aspects of prevention, detection, diagnosis, treatment and survivorship be addressed. This necessitates a DRP committee with diverse representation that works to attract candidates and developmental projects spanning all research and clinical disciplines. The aims of the DRP are to:
1. Stimulate research efforts that include multidisciplinary interactions with clinical and basic scientists inside and out of the participating institutions, including inter-SPORE interactions
2. Provide 1-2 years of developmental project funding for the most innovative investigator-initiated projects in all areas of translational breast cancer research
3. Target funds to specific areas that are especially likely to advance the translational research goals of the SCC Breast SPORE
4. Monitor developmental projects so that one or more are in a position to replace full projects that either complete their aims or are not progressing satisfactorily

Career Development Program

Director:             Martin (Mac) Cheever, MD

Goals of the Seattle Cancer Consortium (SCC) Breast SPORE Career Development Program (CDP) are as
1. Provide research support for advanced fellows, junior faculty and established investigators who wish to develop or refocus their careers on translational breast cancer research
2. Provide a system for mentoring faculty pursuing breast cancer research in a broad range of disciplines
3. Create a framework in which investigators can gain exposure to, and possibly training in, aspects of translational breast cancer research outside their areas of expertise (e.g., a molecular biologist would be exposed to clinical issues in breast cancer care by attending tumor boards and clinical breast cancer conferences)
4. Provide a mechanism by which innovative ideas can develop into promising translational studies in breast cancer research
5. Help attract and retain women, minorities and developing faculty who can make key contributions to translational breast cancer research at the Fred Hutchinson Cancer Research Center (FHCRC) and University of Washington (UW)
6. Create a synergistic environment for translational breast cancer research with other SPORE programs nationwide

Fred Hutchinson Cancer Research Center is a world leader in research to prevent, detect and treat cancer and other life-threatening diseases.