The response of advanced stage breast tumors to treatment is influenced both by omic features intrinsic to the tumor and by the diverse microenvironments in which the tumor cells reside. Omic analyses provide comprehensive “ensemble” views of important intrinsic and extrinsic molecular changes and have been linked to response to individual therapeutic response. The result of an in vitro assessment of intrinsic omic features and therapeutic response gained by analysis of breast cancer cell lines will be presented. However, these measurements are not sensitive to the multi-scale spatial organization of cells and proteins within tumors and their microenvironments. We have begun to explore the importance of the multi-scale spatial intrinsic and extrinsic heterogeneity in therapeutic response via analysis of primary tumors and breast cancer cell lines with emphasis on proliferation and differentiation status. These endpoints were assessed for cell lines grown in different microenvironments using high content fluorescence microscopy after immunofluorescence staining for proliferation and differentiation endpoints. This these studies demonstrate the importance of tumor intrinsic and extrinsic heterogeneity on therapeutic response. We also will present evidence obtained using light and electron microscopy that nanometer sized structures play a role in cell-cell interactions and signal transduction.