In May 2007, the establishment of the first dedicated PLGA research program at the Dana Farber Cancer Institute. The initial $2 million grant will concentrate resources on research on pediatric low-grade brain tumors, in order to discover new and improved targeted therapies that don’t risk impairing children’s bodies and minds. This is believed to be the first coordinated research effort committed to this specific type of tumor world-wide.

This flagship program, under the direction of Charles Stiles, PhD, and Mark Kieran, MD, PhD, draws resources, including personnel and technology, from Dana-Farber’s pediatric neuro-oncology program, the Department of Neurobiology at Harvard Medical School, Children’s Hospital Boston, and the Broad Institute of MIT and Harvard.

Scientists from a range of specialties will focus on clinical and basic aspects of the problem, with a five-year goal of identifying a molecular target in low-grade astrocytomas that can be hit with a designer drug.

Projects include:

Exelixis Partnership: New project, as of 3/08 involves working with a development-stage biotech company called Exelixis. This company has an uncommonly rich pipeline of twelve cancer fighting compounds in clinical development with many more advancing to the clinic. In this project, The Dana Farber will perform pre-clinical experiments necessary to determine if 40 of their most promising compounds show potential for treating JPA.

Oncomap Genetic Profiling: New projects, as of 1/08, involves research on genomics technologies to identify mutations in cancer cell DNA, and to understand how those mutations might make cancer cells vulnerable to new targeted therapies. This study will develop a novel genetic and chemical screening approach to identify changes in malignant melanoma tumor cells that could be targets for new treatments.

Zebra Fish Model: Dr. Thomas Look, Pediatric Oncologist at the Dana Farber Cancer Institute leads the Zebra Fish Facility in altering the zebra fish model to include PLGA brain tumors. The purpose of the study is to accelerate the testing of EXISTING drugs on the PLGA tumors by using the zebra fish as test models. The outcome of these tests will help guide researchers to focus on specific drugs that can then be tested in more sophisticated animal models.

 

Immunohistochemical Analysis: In 2005, immunohistochemical analysis of 78 pediatric brain tumor samples led to the development of data for clinical trials for two promising biological therapies – AZD2171 and CCI779. In fact, a Phase I clinical trial of AZD2171 in children with recurrent or progressive central nervous system tumors was recently opened through the Pediatric Brain Tumor Consortium, and a second trial with this agent has been proposed for children specifically with recurrent low-grade gliomas.

Gene expression studies of gene chips built from paraffin-embedded archival samples of LGG tumors. The preliminary genomic study includes 86 samples, with both type 1 and type 2 low-grade gliomas represented. All samples are archival samples from a patient population representing 20 years of clinical history and therapy outcomes. The goal is that the pilot study will reveal which genes in the LGG tumors are more or less active (up- or down-regulated) compared with normal brain tissue. Dr. Mark Kieran, in conjunction with the Broad Institute at MIT (and with Todd Golub, M.D., along with a dedicated Pediatric Neuro-Pathologist) initiated a novel method of paraffin section RNA analysis. The Broad Institute will use a new methodology to analyze a total of 96 samples simultaneously, a methodology that requires analysis within 48 hours of cutting. Three (3) pathologists will coordinate with the Broad to carry out this process. If we determine genes that are either up- or down-regulated, and the genomic changes are relevant in other words, they are directly linked to tumor development and growth ֖ we will stain tumor samples for the proteins produced by the genes highlighted in the expression studies.

Proteomics: Seldi-TOF: The Seldi-TOF technology provides advantages in the high throughput screen of known proteins in multiple samples. This technique can be used for serial samples from a single patient, or for comparing samples between multiple patients. To provide rapid data on proteins implicated in pediatric low-grade gliomas, CSF samples from patients with low-grade gliomas are being obtained and stored. Preliminary data is being generated using 8 cerebral spinal fluid samples that were sent for standardization of the Seldi-TOF platform for analysis of VEGF. This molecule was selected based on preliminary work demonstrating the presence of VEGF and the activated form of the receptor for VEGF (called VEGFR2) was also identified in all of the pediatric low-grade glioma samples tested (but absent in normal brain). Equally importantly, this association suggests that the two molecules are interacting with each other and may therefore be important in the pathogenesis of this disease.

Proteomics: Maldi-TOF: In contrast to Seldi-TOF technology, where the protein chip platform selected depends on the specific protein you want to analyze, Maldi-TOF is better suited to an analysis of the entire protein complement within a fluid or tissue. Not surprisingly, the complexity of the proteins in a sample can require fractionation of the proteins before analysis. While this dramatically increases the time to analyze each sample, as well as the cost, it is ideally suited to discover new proteins, or proteins not normally present in the tissue or fluid being analyzed. This technique could therefore provide a strategy for the identification of new molecules that are related to tumor initiation, progression, therapy response, and cure versus recurrence. A pilot study of 8 samples was sent for this analysis, all from children with brain tumors (although not all from patients with low-grade gliomas). Initial analysis has been completed and malignant tumor markers were identified, and sub-fractionating work is now being conducted at the Harvard Proteomic Core Facility at Beth Israel Deaconess.

For more information on the PLGA program at Dana-Farber.