Bioinformatics Approaches to Understanding the Breast Cancer Microenvironment

Breast cancer is a complex disease that requires the acquisition of several traits in order to proliferate and spread to nearby and distant tissues. However, many combinations are possible, making it harder to determine their significance. Genome-wide approaches such as gene expression profiling have provided an unbiased and global tool to investigate those traits, allowing investigators to both separate tumors into biologically meaningful categories and then to investigate their features in that context. A well-organized effort is required in order to collect and analyze the large number of samples necessary for such analyses. The Bioinformatics Integrated Application Software represents a way to facilitate both the organization of laboratory manipulation and automating subsequent analyses.;Numerous interactions occur between the various components of the tumor microenvironment. Using matched expression profiles of these cell types, it is possible to identify specific processes that involve several cell types, such as Th1 and Th2 immune responses. This first step will open the door to a better mapping of the interactions and signals that occur in breast cancer.;A large part of the complexity of breast cancer comes from the different types of cells that constitute the microenvironment and participate in diverse ways to tumor progression. Blood vessels play an important role in tumor progression, as additional vessels are necessary to support tumor growth. However, those new vessels are generally immature and often cannot efficiently provide nutrients to the tumor. This thesis shows that there exist two classes of tumor blood vessels that are associated with vessel maturity and differ in their expression of several antiangiogenic drug targets.