Abstract 1616: Phosphoprotein enrichment pathway analysis tools for studying cancer signaling

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Cancer development and progression is driven by dysregulated signaling transduction, which is predominantly regulated by serine, threonine, and tyrosine phosphorylation. Consequently, MS-based phosphoproteomics, which can identify and quantitate thousands of phosphopeptides, provides a powerful quantitative tool to detect and comprehensively catalog alterations in cancer signaling cascades that cannot be captured by analysis of DNA or RNA alone. Unfortunately, the complexity of the datasets generated by these advanced proteomic methodologies are still not matched with well-established or fully tested bioinformatics tools to extract critical pathways from these high-dimensional phosphoprotein data. Here, we present two approaches for identifying pathways with altered phosphorylation patterns: Protein Set Enrichment Analysis (PSEA) and Protein Interaction Enrichment Network Analysis (PIENA). Development of these tools was inspired by two published methods utilizing gene expression datasets to identify disrupted gene sets: Gene Set Enrichment Analysis (GSEA) and Gene Interaction Enrichment Network Analysis (GIENA), respectively. PSEA, through pathway scoring, extracts pathways that show a uniform directional phosphorylation change through all protein members of that set. As in the traditional GSEA method, an enrichment score is calculated for each pathway based on intensity values from all detected phosphopeptides. The second method, PIENA, looks for notable differences in phosphorylation between phosphopeptide pairs. Ultimately, this approach identifies pathways enriched with altered phosphoprotein interactions. Both methods have been used to identify changes in signaling states for two lung adenocarcinoma cell lines, A549 and H358, treated with either control or a novel phosphatase activator with anti-cancer properties. Both PSEA and PIENA identify pathways classically implicated in cancer, including p53, mitosis and cell cycle progression, insulin secretion, immune regulation, and RAS signaling cascades. Furthermore, the ERK pathway is consistently found to be significantly disrupted in both A549 and H358. This corroborates biological findings that this novel drug has activity against KRAS mutated cell lines. Although future cellular experiments will help to confirm the detailed mechanism of this drug's effects, our current results demonstrate the advantage of these new pathway identification tools in providing unbiased and global identification of key drivers of signaling. Citation Format: Danica Wiredja, Yu Liu, Daniela Schlatzer, Giridharan Gokulrangan, Goutham Narla, Mark Chance. Phosphoprotein enrichment pathway analysis tools for studying cancer signaling. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1616. doi:10.1158/1538-7445.AM2014-1616