Breast cancer is a heterogeneous disease with variable clinical presentation, histological features, and response to therapy. Most patients are treated with standard of care chemotherapy, surgery, and/or radiation therapy. Nevertheless, while some patients present favorable treatment responses, others can develop the metastatic disease as early as within the first 3 years after their initial diagnosis. While these differences have been partially explained by intra-tumoral heterogeneity at the genomic and transcriptomic level, the role of spatial and temporal heterogeneity upon disease progression, represented by the tumor architecture is still poorly understood. Moreover, among different cancer types, there are certainly common unanswered medical-biological questions, such as tumor initiation, residual disease, and metastatic disease. Here, we provide a translational insight into the use of cutting-edge technologies that are available to interrogate these questions.