Breast cancer proteomics

Abstract

Breast cancer is still at the top of statistics for incidence and for scientific publications. This testifies the urgency for a better understanding of the biology and the molecular basis of the tumor onset and progression, in order to improve diagnostic and therapeutic strategies. From a biological point of view, the mammary gland, which undergoes cyclical morphogenesis, represents a valid model to study gene expression, epigenetic, differentiation, and cancer. A valid support to these types of research is the proteomic methodology, which over the last decades has been increasingly applied for large-scale detection of protein pathways and pathological biomarkers. This chapter proposes the application of two complementary approaches, ex vivo and in vitro, for the identification of proteins and protein clusters, likely to be correlated with spontaneous or induced phenotypic perturbations representative of neoplastic cells and tissues. Generally, the first goal is the establishment of a reference model for data mining through a platform of consolidated data. The proteomics methodology offers at present a large variety of protocols for gel-based and gel-free applications to the large-scale protein detection, each of them supported by the appropriate reference models. In cases of 2D gel-based proteomics, a reference proteomic map is constructed with computerized applications of the gel-matching procedure among N-numbers of replicate maps. In cases of cancer surgical tissues, a trustable reference is the healthy tissue surrounding the tumor. With this procedure, in our laboratory, we have identified sets of proteins preferentially expressed, or overexpressed, in the tumor tissues, after normalization with the actin content in each map, as cellularity index. Results from surgical explants ex vivo of ductal infiltrating carcinomas, cryo-preserved in our tissue bank, highlighted the appearance of ubiquitous and sporadic proteins. The identity of these proteins, assessed by mass spectrometry and immunologically validated, is discussed in this chapter on the light of literature data, with the aim of finding spontaneous tumor markers able to predict the cancer behavior. The second type of approach, based on in vitro models, is utilized by a large number of researchers worldwide to study cell behavior under basal and experimental conditions. In this chapter some examples of proteomic modulation under experimental conditions, mimicking selected aspects of the in vivo cancer progression, are presented. These aspects regarded the influences exerted by tumor-related collagens used as substrates for neoplastic cell cultures, the effects of fibroblast cocultured with the cancer cells and those exerted by transgenic decorin, a small leucine-rich proteoglycan with putative antioncogenic properties. Finally the proteomics of secreted vesicle and the responses to the biopharmacological drug trastuzumab were described. The proteins involved in each situation are commented on the basis of current literature. Conclusively, the contribution of proteomics in recognizing hundreds of proteins involved and responsive to the internal/external tumor environment appears a winning strategy if conducted in a highly controlled way with precise reference points.