Progress Report Cancer Research Foundation January 1, 2009 – December 31, 2010

Title: Defining the Role of MYCN in High-Risk Neuroblastoma Using Quantitative Proteomics

PI: Samuel L. Volchenboum, MD, PhD University of Chicago Assistant Professor of Pediatrics and Computation

KCBD 5130, 900 E. 57th Street Chicago, IL 60637

Phone: 773-769-7433 Fax: 773-834-1329

Email: slv@uchicago.edu

Lay Summary My lab is interested in understanding how amplification of the MYCN oncogene leads to aggressive neuroblastoma. It has long been known that patients with tumors that harbor many copies of this gene do very poorly, but the mechanism for this has not been well described. We are using mass spectrometry to describe the proteins produced in neuroblastoma cells, so that we can compare high MYCN producing cells with those that produce normal levels. In this way, we hope to better understand how aggressive tumors grown uncontrollably and evade treatment. We have identified a panel of proteins that are differentially expressed, and we have confirmed these findings with other methods. We are probing patient tumor samples for these proteins as well, in order to validate our findings. We have also investigated our tumor cells with gene expression profiling, in order to compare the genes transcribed with the proteins produced. These data should give valuable insight into how neuroblastoma is able to grow and metastasize despite aggressive multimodal therapy. Discoveries made about the protein pathways involved in tumor development will allow better patient diagnosis and therapy, leading to improved outcomes for patients with neuroblastoma.

Summary The central hypothesis of this study is that a specific protein signature defines MYCN-amplified high-risk neuroblastoma and that understanding the differences in specific patterns of protein expression between neuroblastoma tumors will allow for better patient diagnosis, stratification and treatment. Furthermore, proteomic techniques developed through this work will permit better assessment of intermediate endpoints of therapy. Progress in these areas will improve outcomes for children with neuroblastoma.

Specific Aims To the end of assessing this hypothesis, the following specific aims are proposed:

Specific Aim 1: To compare the pattern of protein expression in cell lines that over-express the MYCN oncogene with cell lines that do not. Quantitative mass spectrometry will be utilized to facilitate a description of the expressed proteins in established neuroblastoma cell lines that do and do not exhibit MYCN overexpression.

Specific Aim 2: To validate the differential expression of proteins identified in Aim 1 in samples from patients with neuroblastoma. Antibody-based methods of protein detection will be used to validate proteins identified in Aim 1 in tumor samples from patients with neuroblastoma acquired from the Children’s Oncology Group (COG) tumor bank. The validated set of proteins will be used to better describe the biological pathways underlying aggressive neuroblastoma.

Update – Final:  The funds generously provided by the Cancer Research Foundation have allowed us to produce a manuscript entitled, “Proteomic Analysis of Neuroblastoma Cells identifies MYCN-Regulated Proteins and Pathways.” This work has been submitted for publication, and we are currently revising the manuscript for resubmission based on the reviewers’ comments. A copy of the manuscript is attached for your review. I will send a final version once it is accepted for publication. Again, your support has allowed us to generate important data that will inform future experiments. Already, we have entered into successful collaborations with Garrett Brodeur at Children’s Hospital of Philadelphia and Samir Hanash at MD Anderson. Ultimately, we hope to apply these data for extramural funding.