Proteomic Profiling of Infiltrating Ductal Carcinoma Reveals Increased Cellular Interactions with Tissue Microenvironment

Progression of invasive carcinoma involves the deregulation
of molecular signaling pathways that results in the acquisition of
oncogenic phenotypes. Functional enrichment analysis allows for the
identification of deregulated pathways from omics scale expression
data. Given the importance of post-transcriptional regulatory mechanisms
on protein expression and function, identification of deregulated
pathways on the basis of protein expression data is likely to provide
new insights. In this study, we have developed methods for label-based
mass spectrometry in a large number of samples and applied these methods
toward identification and quantification of protein expression in
samples of infiltrating ductal carcinoma, benign breast growths, and
normal adjacent tissue. We identified 265 proteins with differential
expression patterns in infiltrating ductal carcinoma relative to benign
growths or normal breast tissue. Analysis of the differentially expressed
proteins indicated the deregulation of signaling pathways related
to proliferation, invasion and metastasis, and immune response. Our
approach provides complementary information to gene expression microarray
data and identifies a number of deregulated molecular signaling pathways
indicative of breast cancer progression that may enable more accurate,
biologically relevant diagnoses and provide a stepping stone to personalized
treatment.