A Proteomic Dissection of Breast Cancer - Via Cells and Organelles to Pathways

Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death in females worldwide. Breast tumours are extremely heterogeneous, and each patient’s disease has different causes, prognosis and appropriate treatments associated with it. To enable a more individualised therapy, there is a substantial need for better characterisation of tumours and a deeper understanding of the molecular mechanisms of disease initiation, progression and treatment resistance. During the last decade, shotgun proteomics has evolved as a powerful tool, complementing the fields of genomics and transcriptomics, for the elucidation of pathway and network changes in cancer. The proteome is, however, with its large dynamic range and numerous post-translational modifications, tremendously more complex than the genome and an additional level of complexity is provided by the spatial arrangements of proteins in different organelles. In this thesis we have addressed technical challenges such as optimising proteomic coverage by evaluating different protein and peptide separation methods and mapping proteins to organelles with density gradient organelle fractionation followed by proteomic quantification of the fractions. Further, we applied both a discovery mode of proteomics and a focussed pathway centric method to evaluate the response of breast cancer cell lines to chemotherapeutic agents. Proteomic pathway analysis was also utilised to investigate and explain the differential response to therapy in different breast tumour subpopulations