Novel quantitative proteomic approaches to reveal new driving mechanisms and biomarkers of tumorigenesis

Understanding the biological processes and pathways important to healthy and disease states requires the probing of systems at the protein level. While genetic alterations may predict the likelihood of disease, it is the phenotypic changes which characterize disease onset. The growth of mass spectrometry-based proteomics over the past two decades has been essential for our ability to perform systems-level interrogations of both healthy and disease states. Here, we have employed quantitative proteomic techniques to investigate breast cancer and glioma biology. Chapter 1 provides background on breast cancer heterogeneity and the challenges in classifying breast tumors in a clinically relevant manner. It additionally presents an overview of mass-spectrometry based proteomics and methods of proteomic quantitation. Chapter 2 presents a novel workflow for the identification of new liquid biopsy biomarkers for breast cancer prognosis. We developed a multi-omic approach linking oncogenic secreted proteins to patient-specific transcriptomic data and clinical outcomes. Kaplan-Meier analysis of genes having a secretion correlated expression pattern was used to identify new liquid biopsy biomarkers for predicting individualized prognosis. Chapter 3 explores the role of spliceosome protein SNRPD1 in breast cancer. SNRPD1 is often overexpressed in breast cancer and plays a seemingly important, but understudied, role in tumor aggressiveness. We have performed the first systems-level study of SNRPD1 function in breast cancer cells and identify previously unreported signaling pathways and biological functions impacted by SNRPD1. Chapter 4 introduces a novel approach to the study of secreted proteins termed outside-in proteomics. We first perform an unbiased screen of the secretome to identify phenotypic-relevant markers and use those results to guide our investigation of the intracellular proteome. We applied this approach to analyze the role of EZH2 in the aggressive phenotype of triple negative breast cancer. Chapter 5 presents a quantitative proteomic comparison of IDH1 mutant and wild type glioma cells. We performed a proteomic screen of IDH1 mutant versus wild type gliomas, and we report several new pathways and processes which may contribute to IDH1 mutant glioma pathogenesis or progression. Overall, this work demonstrates both novel and traditional mass spectrometric proteomic techniques for the investigation of human disease.Doctor of Philosoph