Abstract 4873: Protein complexes in cancer: A novel strategy to identify protein complexes through reduction of false discovery rate

Abstract

Abstract Most cellular processes are controlled by protein-protein interactions, and aberrant protein-protein interactions can lead to human diseases such as cancer. Hence a comprehensive understanding of a protein interaction network and its dynamics response to different physiological conditions is essential for understanding a protein's function and may reveal novel therapeutic opportunities for fighting cancer. Affinity purification coupled with mass spectrometry has become the method of choice to study in vivo protein interactions and formation of protein complexes. However, the methodology has some limitations that reduce it application such as, under sampling of low abundant proteins and high background leading to an elevated false discovery rate (FDR). Herein we describe a strategy utilizing differential expression of the target protein followed by analysis using quantitative proteomics. By performing affinity purification on cells expressing increasing amounts of the polycomb complex protein Bmi-1, we show that known interacting proteins could be distinguished very efficiently from the background proteins based on their abundance profile. Applying this method to the data set significantly reduced the FDR and allowed us to identify potentially new interacting proteins for Bmi-1 that otherwise would have been considered non-specifically bound proteins. The method was also applied to characterize the interactome for Snail I, II and III a family of Zn-finger proteins thought to be involved in transcriptional repression. These proteins have been implicated in diverse biological function such as regulation of epithelial to mesenchymal transition, formation and maintenance of embryonic mesoderm, generation and migration of neural crest cells and metastasis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4873. doi:10.1158/1538-7445.AM2011-4873