Abstract LB-35: Reconstructing targetable pathways in lung cancer by integrating transcriptome, proteome and phosphoproteome (2012)

Abstract Lung cancer is the leading cause of cancer mortality in the United States, and non-small cell lung cancer (NSCLC) is the predominant subtype of this malignancy. Mutations in the KRAS oncogene characterize more than 20% of all NSCLC malignancies, and recent studies suggest that those tumors could be divided into two molecular classifications: KRAS dependent (KRAS-Dep) and KRAS independent (KRAS-Ind), according to their dependency on KRAS mutant for cell survival and proliferation. Although, the KRAS signaling pathway has been extensively characterized using high throughput transcriptomic or proteomic technologies in isolation, the specific network of effector genes and proteins that drives carcinogenesis in NSCLC is still far from being understood. In this study we have generated and integrated a matched global phosphoproteome, proteome and transcriptome data set for a panel KRAS- Dep and KRAS-Ind NSCLC cell lines. Gene expression, protein abundance and protein phosphorylation were quantified for each of the 12 cell lines using RNA-sequencing (RNA-seq) and label-free quantitative tandem mass spectrometry (LC-MS/MS) respectively. We use a Prize Collecting Steiner Tree (PCST) algorithm in order to reconstruct active and targetable pathways associated with KRAS dependency. This algorithm allows us to synthesize transcriptome, proteome and phosphoproteome signatures with a human protein-to-protein interaction network (PPI) derived from public repositories. By using this approach we have nominated, and validated, several druggable kinases that are activated in KRAS-Dep but not in KRAS-Ind NSCLC cell lines. Specifically, this study indicates that KRAS Dep cell lines have an active and druggable pathway constituted by the lymphocyte specific tyrosine kinase (LCK), KRAS, and the p21 protein (Cdc42/Rac)-activated kinase 1 (PAK1). The activation of PAK1 could confer both sustained growth and the ability to modulate cell's motility, and therefore this pathway could be essential for KRAS dependent cells. In congruence with this, previous reports have suggested moderate to high expression of PAK1 protein in ∼ 20% of NSCLC adenocarcinoma tumors (Ong, C., et al PNAS April 11: 1-6). Additionally, a second but independent pathway constituted by active and stable Beta-catenin (CTNNB1), E-Cadherin (CDH1) and Alpha-Catenin (CTNNA1) also characterizes the KRAS-Dep phenotype. Those proteins belong to the catenin/cadherin/PSEN adhesion complex and play a crucial role in cell differentiation, which could explain previous observations relating KRAS dependency with a more differentiated phenotype (Singh, A., et al Cell 15: 489-500, 2009). In summary in this study, we are establishing a druggable pathway that is active in the KRAS-Dep but not in the KRAS-Ind phenotype, and so defining new potential druggable targets for treating KRAS dependent lung cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-35. doi:1538-7445.AM2012-LB-35