Abstract 5125: Proteomic profiling reveals increased immunological response and extracellular matrix-receptor interactions in invasive ductal carcinoma

Background: 70% of breast cancer cases diagnosed are infiltrating/invasive ductal carcinoma. The progression of normal cells to non-malignant cells or to invasive cells involves dysregulation of a range of cellular processes and molecular signaling pathways. Identifying these pathways and the specific proteins involved will lead to better understanding of disease processes and more specific diagnoses and better treatment outcomes. The aim of this study is to identify changes in protein expression and related pathways between malignant/invasive, non-malignant and normal adjacent-to-tumor tissue from patients diagnosed with non-invasive breast disease or infiltrating ductal carcinoma. Methods: 90 frozen tissue samples from the Kimmel Cancer Center tissue bank, including 26 malignant, 30 non-malignant, and 34 normal-adjacent-to-tumor samples, were embedded in OCT and cut into 15-micron sections. Proteins were processed using a Filtration-Aided Sample Preparation approach in 96-well filter-plate format. The tryptic digests were labeled with iTRAQ-8plex tags and combined into 13 sets, each with a pooled internal reference. Labeled peptides were subjected to 2-D LC-tandem MS and ProteinPilot analysis. Algorithms were programmed in-lab for data normalization and protein quantification. The DAVID (Database for Annotation, Visualization and Integrated Discovery) tool identified signaling pathways associated with differentially expressed proteins. Results: Over 1000 proteins were identified with approximately 20 % of the proteins differentially expressed in malignant or non-malignant samples compared to the normal adjacent-to-tumor. Hierarchical clustering clearly illustrated a separation between the malignant, the non-malignant, and the normal adjacent-to-tumor tissue types. Pathway analysis comparing differentially expressed proteins from malignant and normal adjacent tissues revealed the enrichment of extracellular matrix-receptor interaction and focal adhesion processes, consistent with the invasive phenotype. Pathways associated with immune response and angiogenesis were also indentified in comparison across the three tissue types. Conclusion: The pooled internal reference enabled quantitative analysis of 90 samples in the present study. The differentially expressed proteins may act as potential biomarkers for tissue classification, diagnosis, and treatment plan decisions. Bioinformatics analysis revealed the changes in protein expression are related to pathway