2D Gel-based Proteomics Research Articles

Proteomic Characterization of Angiogenic Endothelial Cells Stimulated with Cancer Cell-Conditioned Medium

To characterize the protein expression profiles and identify the molecules associated with tumor angiogenesis, the cellular proteins of human umbilical vein endothelial cells (HUVECs) in response to cancer cell-conditioned medium (CM) prepared from HT1080 human fibrosarcoma cells were analyzed using fluorescence-labeled 2D gel-based proteomics. Most differentially expressed proteins in HT1080-CM-stimulated cells were found to be downregulated (88%) rather than upregulated (12%) based on statistical analysis of protein spot signals. Additionally, we examined the effects of vascular endothelial cell growth factor (VEGF), a proangiogenic factor, on cellular protein expression. In contrast, most differentially expressed proteins were found to be upregulated (59%) rather than downregulated (41%) in VEGF-stimulated HUVECs. Comparative analyses of 29 and 35 protein species identified in CM-stimulated and VEGF-stimulated HUVECs, respectively, revealed the remarkable differences between these two stimulations. Only four proteins were differentially expressed by both treatments: annexin A2, enolase 1, and T-plastin (downregulated by CM but upregulated by VEGF), and RAN (downregulated by both CM and VEGF). These findings provide new information regarding the regulation of protein expression associated with tumor angiogenesis.

A software utility for creating interactive maps for 2D gel-based proteomics

A software utility for creating interactive maps for 2D gel-based proteomics

The application of 2D gel-based proteomics methods to the study of breast cancer.

The protein complement of breast cells consists of many thousands of proteins. Recent developments in 2D gel electrophoresis technology have made studies requiring the quantitative analysis of a differential proteome, such as comparison between normal and malignant cells or investigation of drug effects on cells, truly feasible. Computer software plays a central part in the comparisons between multiple gels required for such experiments. In addition, software tools allow patterns of coexpression of proteins to be studied, offering potential insights into protein regulation, interactions, and functions, especially when combined with complementary data on gene expression. In this paper, the technology and limitations of 2D gel-based proteomics are reviewed. Techniques for comparing sets of gels at a global level as well as identifying specific protein features that differentiate gels are discussed. Our own experience of studying the breast cell proteome is used to illustrate the difficulties and achievements of differential proteomics.