Proteomics of cancer stem cells

New understanding of cancer stem cell (CSC) biology continues to emerge due to development of novel methods in genomics and proteomics. Analysis of nucleic acids (RNA, DNA) is widely used to elucidate molecular perturbations in malignant tumors and carcinoma cells, however genome data do not reflect the functional activities of encoded proteins. Therefore proteome-based methods could enhance knowledge about deregulation of pathways as a result of altered expression and activities of proteins in CSC.

A sufficient number of CSC for proteomic analyses can be obtained in a variety of ways: Fluorescence (FACS) and magnetic (MACS) activated cell sorting, laser cell capture microdissection, and three-dimensional spheroid/organoid cell culture. These methods to enrich and isolate CSC can be performed either with or without staining using antibodies against currently known CSC-specific cell surface molecules, such as clusters of differentiation 44, 24, 133 (CD44, CD24, CD133), epithelial cell adhesion molecule (EpCAM), aldehyde-dehydrogenase-1 (ALDH1), etc. The most important limitation on using antibody-based staining of CSC is that we still do not possess definitive CSC surface markers. This review article discusses methods that could be used to study protein profiling of CSC and to identify novel CSC-specific biomarkers and therapeutic targets.

Despite an opinion that the proteomic approach is time-consuming, laborious and difficult, this method can be used effectively to clarify which pathways are involved in regulating various intratumoral processes, including activation of CSC. Based on this point of view, searching and identification of single molecules as biomarkers or therapeutic targets could become possible when CSC-associated pathways are well described and clearly understood due to detailed investigation of the protein patterns in pre-clinical models and clinical samples.