Proteomics is now entering into the field of biomedicine with declared hopes for the identification of new pathological markers and therapeutic targets. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of low-abundant proteins. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration of related pathologies paved with various difficulties and pitfalls. The case of breast cancer illustrates the major challenge facing modern proteomics and more generally post-genomics: to tackle the complexity of life. Molecular & Cellular Proteomics 2:281-291, 2003.During the last several years, the field of proteomics has evolved considerably. Traditional two-dimensional (2D) 1 electrophoresis (2DE) has been improved and new off-gel methods have been developed. At the same time, mass spectrometry not only allows protein identification with increasing sensitivity, but also the precise exploration of protein-protein interactions and post-translational modifications, such as phosphorylation. A further major step has been large-scale, high-throughput analysis, rendering possible the description and functional investigation of proteomes. In biomedicine, this has led to considerable hope for the identification of potential pathological markers and therapeutic targets (1, 2), particularly in the field of cancer (3). However, the biggest impediment to proteomic analyses remains biology and its intrinsic complexity. After genome sequencing and now proteome characterization, it appears that large-scale analysis tools are still not sufficient to resolve biological issues. This is well illustrated with breast cancer, a major form of cancer, for which some aspects of proteomics are opening new perspectives. Despite the establishment of tissue data bases and the use of state-of-the-art proteomic technologies, the complex biology of the mammary gland, as well as of breast tumors, remains a major limitation to the full deployment of proteomic tools and the successful realization of their theoretical power.
CHALLENGES FACING RESEARCH ON BREAST CANCERThere are two main expected outcomes from proteomic analyses of breast cancer. The first is to discover new molecular markers for early diagnosis and profiling of breast tumors. The second is to decipher the intracellular signaling pathways leading to the initiation and progression of breast tumors. Such data should provide the knowledge base for the identification of new therapeutic targets and the development of innovative strategies against breast cancer.Current methods used to detect breast tumors, either benign or malignant, are based on mammography. However, there are intrinsic limitations to mammography. First, there are suggestions that X-rays can potentially induced carcinogenesis, and second, it is clear that to be detected in mammography, a breast tumor should be at least a few millimeters in size. ...