Brain Tumor SPORE
University of California, San Francisco
Mitchel S. Berger, M.D.
PROJECT 1: THE SAN FRANCISCO BAY AREA ADULT GLIOMA SURVIVAL STUDY
Margaret Wrensch, Ph.D.
John Wiencke, Ph.D.
The goals of this continuing Adult Glioma Survival Study are to identify new germline genetic traits that affect the survival of patients with diverse types of glioma and to integrate these heritable factors with the most recently discovered tumor molecular features that affect survival. To accomplish this we will apply a genome wide association approach to a large population of UCSF, Mayo and TCGA glioma cases and controls. We will confirm and extend our studies using a collaborative network including the Southeastern US glioma study population (GliomaSE). We will apply a powerful and highly efficient single nucleotide polymorphism (SNP) genotyping platform (Affymetrix 640K Axiom array) to 820 glioblastoma patients and replicate our findings in 693 GBM patients. Only GBM patients treated with standard of care surgery, radiation and temozolomide will be included to minimize variations in treatment on patient outcomes. We will also carry out the first genome wide survival studies in grade II and III infiltrating glioma, using a large population of 1749 cases. Grade II and III patients have substantially longer survival times compared with high grade GBM and offer an even greater chance to uncover new inherited factors important for survival. We will also apply the results of these discovery analyses in grade II and III glioma patients in long standing completed clinical trials to begin to assess the generalizability of our findings to clinical trial populations. Finally, we will use our extensive tumor molecular database for to assess inherited genetic survival factors in glioma molecular subtypes. We have data on the IDH and TP53 mutation status, EGFR amplification and MGMT methylation of tumors that will be combined with inherited genetic information to carry out the first ‘integrative’ genomics’ study of glioma survival. Building on 10 years of SPORE funding and over 20 years of R01 funding and our extensive and productive ongoing collaborations, this proposal will uncover new patient and tumor prognostic factors for glioma. Understanding their relationship to known factors is crucial not only for greater understanding of glioma pathogenesis and providing accurate assessment to patients about their prognosis, but also potentially for optimal patient stratification for treatment.
PROJECT 2: NOVEL BIOMARKERS OF MALIGNANT PROGRESSION IN RECURRENT LOW GRADE GLIOMA (LGG)
Susan Chang, M.D.
Joseph Costello, Ph.D.
Sarah J. Nelson, Ph.D.
The goal of the proposed study is to evaluate the role of noninvasive imaging parameters as biomarkers of malignant transformation in diffuse low grade glioma and to use these parameters to select regions for characterizing the genetic mutations associated with recurrent disease. The studies will have a significant impact on the management of these patients by providing objective criteria to predict when a lesion transforms to a more malignant phenotype, whether and where to intervene surgically and how to select the next line therapy. This is an important problem because patients with tumors that recur from a prior LGG have different outcomes depending on histological subtype, grade, and molecular/cytogenetic features. The mechanisms of malignant transformation are unclear and treatment strategies are often pursued without histological confirmation of recurrent tumor. In our previous SPORE Project, we applied magnetic resonance imaging (MRI) and spectroscopic imaging (MRSI) to evaluate 125 patients prior to resection of tumors that were thought to have recurred from a prior LGG. Significant differences in the in vivo MR measures were seen for tumors with malignant transformation compared to those that did not. Ex vivo analysis of the histological status, IDH1 mutations and ex-vivo NMR spectra from the image guided tissue samples provided new information that resulted in novel hypotheses being investigated in Specific Aim 1. Extending this approach by defining the mutation profile using next-generation sequencing of image guided tissue samples with defined histology will increase the probability of identifying mutations that drive malignant transformation and address, for the first time, the tumor genome evolution associated with treatment effects and the natural history of the disease.Specific Aim 1 will relate in-vivo MR parameters to malignant transformation and clinical outcome and Specific Aim 2 will use paired samples from lesions that either do or do not have the characteristics of malignant transformation, as well as paired samples from the current and subsequent surgery to examine the evolution of the mutation profile. The knowledge gained will make a major impact upon patient care.
PROJECT 3: NOVEL APPROACHES FOR IMPROVING PEDIATRIC BRAFV600E GLIOMA PATIENT OUTCOMES
C. David James, Ph.D.
Theodore Nicolaides, M.D.
Michael Prados, M.D.
Backgound and hypothesis. Currently we are faced with a lack of effective, FDA approved interventions to control glioma in children. BRAFV600E mutations occur at significant frequencies in several histopathologic subtypes of pediatric glioma. Small molecule inhibitors specific for BRAFV600E have been developed that show remarkable efficacy in treating BRAFV600E melanoma, and we have recently shown that a BRAFV600E inhibitor significantly extends the survival of animal subjects with intracranial BRAFV600E glioma xenografts. We feel that incidence of BRAFV600E in pediatric patients with glioma combined with the availability of an effective therapeutic against BRAFV600E tumors constitute a compelling basis for testing BRAFV600E therapy in treating children with BRAFV600E brain tumors.
Although we are excited about our results, we have identified feedback mechanisms that help BRAFV600E tumor cells compensate for and ultimately escape BRAF inhibition. However, we have also identified approaches for disrupting compensatory feedback signaling, and that can be used to improve upon the results of BRAF inhibitor monotherapy. Specifically, the use of secondary inhibitors, that target distinct enzymatic activities, and that are administered concurrently with a BRAF inhibitor result in increased anti-proliferative effect and survival extension of animal subjects with intracranial BRAFV600E glioma. These results indicate the need for developing combination therapy approaches for maximizing anti-tumor effect and achieving durable disease relief for pediatric patients with BRAFV600E glioma. This is the objective of our research, as conducted in association with the following specific aims:
Aim 1: Investigate Mechanisms That Limit BRAF Inhibitor Sensitivity in BRAFV600E Gliomas.
Aim 2: Investigate 2-agent combinations for relative efficacy, both with and without concurrent radiation therapy (RT), and analyze tumor specimens for adaptation to sustained treatment.
Aim 3: Evaluate BRAF targeted therapy in patients with BRAFV600E pediatric glioma.
Given the unmet need for improved treatment of this cancer in this patient population, combined with the unique opportunity to target a newly discovered, biologically relevant mutation, and the expertise of our research team in translating laboratory-based findings into clinical action, we will test BRAF inhibitor therapy for pediatric BRAFV600E glioma, and anticipate this research to have significant, positive benefit for children with this currently incurable cancer.
PROJECT 4: OVERCOMING LOCAL AND PERIPHERAL IMMUNE SUPPRESSION IN GLIOMA TO FACILITATE EFFECTIVE GLIOMA THERAPY
Andrew T. Parsa, M.D., Ph.D.
Russell O. Pieper, Ph.D.
The long-term translational goal of this project is to overcome mechanisms of immunoresistance that diminish efficacy of immunotherapy for glioma patients, particularly glioblastoma (GBM). In the previous cycle we completed a Phase I clinical trial and a Phase II clinical trial for recurrent GBM patients immunized with an experimental vaccine, after surgical resection. These trials demonstrated that autologous glioma-derived heat shock protein peptide complex-96 (HSPPC-96) vaccine is safe, evokes a CD4+ and CD8+ tumor specific T-cell response and increases survival of recurrent GBM patients as compared to historical controls. In the previous SPORE cycle we also identified proteins that contribute to glioma immunoresistance, including B7-Homologue 1 (B7-H1) that is expressed on the glioma cell surface, induces CD8+ T-cell apoptosis and is positively regulated by PI(3)K. Our observations explain how the PI(3)K/B7-H1 pathway can directly inhibit T-cell killing of tumor. In the next cycle of this project we plan to test the hypothesis that immunosuppressive tumor effects of PI(3)K/B7-H1 pathway activation can also be mediated indirectly, through expansion of the regulatory T cell (Treg) pool (Aim 1) and through expression of B7-H1 protein on tumor infiltrating macrophages (Aim 2) in patients with low grade astrocytoma (LGA), anaplastic astrocytoma (AA), and GBM. To determine the clinical impact of PI(3)K/B7-H1 pathway activation on response to glioma immunotherapy we will initiate a randomized trial comparing the standard of care (intravenous bevacizumab) to HSPPC-96 combined with bevacizumab in recurrent GBM patients (Aim 3).
CORE A: BIOSPECIMEN / PATHOLOGY CORE
Arie Perry, M.D.
Joanna J. Phillips, M.D., Ph.D.
The Brain Tumor SPORE Biospecimen/Pathology Core provides staff and technology dedicated to enhancing brain tumor biospecimen integrity and usability through use of optimized collection procedures; multi-modality preservation, processing, and analysis; histopathologic-molecular characterization; and computerized inventory and web-based request and tracking systems. All aspects of sample identification, processing and storage are performed with strict compliance to the College of American Pathologists (CAP) guidelines. In order to maximize sharing and integration of SPORE projects, the Tissue Core collects and makes available data derived from all distributed brain tumor biospecimens.
Specific Aims of the SPORE Biospecimen/Pathology Core:
Aim 1: To acquire brain tumor patient biospecimens from the operating room and SPORE Animal Core with optimized handling to maximize cell viability and/or minimize the warm-ischemic interval so as to meet the tissue accrual requirements for the Brain Tumor SPORE projects and clinical trials. This aim is essential for all Projects.
Aim 2: To perform quality control assays on archived brain tumor biospecimens collected from the operating room and SPORE Animal Core, to ensure availability of adequate numbers of consistently handled specimens that will yield high quality data for SPORE projects and clinical trials.
Aim 3: To provide routine and advanced tissue handling/processing and analytical techniques, including immunohistochemistry, fluorescence in situ hybridization (FISH), tissue microarray construction, DNA/RNA extraction, protein isolation, and preparation of viable cells that will advance project hypothesis development and goal attainment.
Aim 4: To maintain a database containing demographic data, results from molecular analyses, and brain tumor patient biospecimen distributions (internal and external) that will be linked to relational clinical databases maintained by the Biostatistics and Clinical Core.
CORE B: PRE-CLINICAL ANIMAL CORE
C. David James, Ph.D.
Tomoko Ozawa, M.D., Ph.D.
Because of the translational requirement of SPORE research, it is essential that SPORE investigators have access to and assistance with animal models for therapeutic hypothesis testing. The UCSF Brain Tumor SPORE Animal Core addresses this need by using 3 types of rodent intracranial engraftment models, based on cell of origin: 1) human tumor cells; 2) chemically induced rodent brain tumor cell lines; and 3) tumor cells derived from genetically modified mouse models. Tumor cells are implanted in the brains of immunodeficient, and/or immunocompetent hosts, with therapeutic effect determined by bioluminescence monitoring of tumor growth, animal subject survival analysis, and immunohistochemical analysis of tumor biologic response indicators, especially proliferation and apoptotic response. In addition, the Core also conducts studies to assess therapeutic toxicity and biodistribution. These studies typically involve organ and tissue harvests at pre-determined timepoints, with specimens examined for drug content, and/or indication of abnormal pathology, and/or abnormal cell counts when blood samples are obtained. Finally, the Core serves as a source of tumor tissues, resulting from engraftment procedures, for biomarker investigation and assay development, and for in vitro investigation in instances involving the transfer of viable tissues or cells.
These activities are carried out in association with the following specific aims:
Aim 1: Propagate, analyze (histopathological and molecular), archive, and maintain up-to-date records on all tumor cell sources and tissues used in support of SPORE animal model research.
Aim 2: Advise and assist all rodent model therapeutics testing, including optical imaging, survival benefit analysis, toxicity assessment, and molecular analyses of tumors for response to therapy.
Aim 3: In association with the Tissue Core, utilize human xenograft tumor tissues to facilitate the development of immunohistochemical and FISH assays that can be applied to the investigation of biologic response indicators, therapeutic targets, and surrogate markers in patient tumors.
Aim 4: Process, and distribute, within and outside of UCSF, xenograft tumor tissues and cell lines, as well as extracts from each, so as to promote intra- and inter-SPORE collaborations, as well as to support brain tumor research in general, through utilization of renewable tumor cell resources.
CORE C: BIOSTATISTICS AND CLINICAL CORE
Annette Molinaro, Ph.D.
Michael Prados, M.D.
The Biostatistics and Clinical Core will provide the leadership and expertise needed to support the laboratory and clinical research of the 4 Projects of this SPORE grant. The Clinical component will be led by Dr. Prados, who will interact with Project leaders to develop clinical trials based upon laboratory investigations in Projects Three and Four in particular, as well as to discuss results in Projects One and Two that may lead to relevant biomarkers and potential stratification factors for future or potential clinical trials. The Clinical component will support the actual conduct of SPORE clinical trials, including providing clinicians, research nurses and data coordinators, and assist in all of the required regulatory reporting for those studies. Dr. Prados will support and facilitate the interactions of Project leaders with CTEP, cooperative groups, biopharmaceutical, and industry groups to obtain new therapeutic agents appropriate to the design of new studies that come from Projects Three and Four, as well as supporting the conduct of SPORE clinical trials to those groups as needed.
The Biostatistical component will be led by Dr. Molinaro, who will interact on an ongoing basis with the individual leaders from all four Projects to assess the statistical needs of each. The Biostatistical component will provide: advice on the design of experimental and clinical studies, including calculating sample sizes and power; data analysis support (either by performing the analyses within the core or advising qualified personnel within the projects), including the use of appropriate statistical models and applications of statistical test; and, when necessary, the development of novel methods to help interpret results from experiments. Additionally, a member of the Biostatistical component will participate in regularly scheduled project meetings to provide statistical/bioinformatics input and assist in preparing the necessary materials for presentation and publication.
CORE D: ADMINISTRATIVE CORE
Mitchel S. Berger, M.D.
Russell O. Pieper, Ph.D.
Michael Prados, M.D.
The UCSF Brain Tumor SPORE proposal has 4 overall specific objectives: 1) to identify factors that contribute to the likelihood of surviving brain cancer; 2) to identify spectroscopic, non-invasively derived imaging parameters and linked tissue biomarkers that can help predict recurrence and outcome in patients with low grade glioma; 3) to develop improved therapies for pediatric brain tumors harboring BRAF mutations; and 4) to improve the immunotherapy of brain cancer. The Administrative Core of the UCSF Brain Tumor SPORE has been created to supervise the activities of the UCSF Brain Tumor SPORE and to provide fiscal management, administrative support, and the framework by which researchers can communicate and interact. The aims of the Core are: 1. To evaluate research progress. The Administrative Core, through the SPORE Executive Committee, the SPORE Steering Committee, and the SPORE External Advisory Board, will be responsible for evaluating the progress of projects and making decisions regarding the continuation/replacement of projects. 2. To provide fiscal management. The Administrative Core will distribute funds from the SPORE Award, the Career Development and Developmental Research Programs, SPORE Supplement Awards, and discretionary funds provided by the institution. The Administrative Core will also be responsible for the timely reporting of finances to Project Leaders and the SPORE PI/co-PIs. 3. To provide administrative support. The Administrative Core will be responsible for the daily operations of the SPORE, for the preparation of SPORE-related manuscripts, and for communications with NIH. 4. To facilitate communication between SPORE investigators. The Administrative Core will be responsible for the scheduling of all meetings, seminar series, and retreats, and for the distribution of the notices inviting participation in the Career Development Program and the Developmental Research Program. 5. To assist in compliance. The Administrative Core will be responsible for assuring compliance and scientific integrity of all components of the SPORE. The Administrative Core will be used by all Projects and Cores in the SPORE.