Abstract 885: Integrated analysis of colorectal cancer cell lines reveals an amplicon driver which may be involved in platinium resistance

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Background: First line adjuvant treatment for colorectal cancer (CRC) is 5-fluorouracil and the platinum compound oxaliplatin. New targeted therapies such as cetuximab and PI3K/mTOR inhibitors are being developed in order to improve therapeutic outcomes. However, intrinsic and acquired resistance is common and selecting patients who are likely to respond remains a clinical and pathological challenge. The aim of this study is to identify new targets for therapy using an integrated genomic, transcriptomic, proteomic, and functional analysis of CRC cell lines. Methods: Cell proliferation assays (AlamarBlue) were carried out on a panel 15 colorectal cancer cell lines. IC50s were established for 5-fluoruracil, oxaliplatin, and BEZ-235, a PI3K/mTOR inhibitor. Cell lines were profiled using reverse phase protein arrays (RPPA) for protein expression, Illumina gene expression analysis, array comparative genomic hybridization (aCGH; NimbleGen 135k chips) and targeted sequencing of hotspot mutations. Associations of mutations, transcript, copy number variations and proteome with drug sensitivity were established using correlation coefficients and integrated network analysis. Validation of copy number gains and losses was performed in primary tumors using Oncomine to interrogate public databases. Results: IC50s varied from resistant to highly sensitive for all three compounds. BRAF V600E mutation was significantly associated with response to 5 fluorouracil (p = 0.006). There were 17 regions of recurrent amplification across 14 cell lines and 48 regions of loss. The frequently and highly amplified regions included 8q24.13 - 8q24.21 which was significantly correlated with oxaliplatin response (p = 0.031), and amplified in 11% of primary CRCs on interrogation of public databases. This amplified region contains the putative oncogene TRIB1, a cell signaling regulator, which was correlated with gene expression across the cell lines and was found to be significantly correlated to the AKT (p=0.026), phosphor-mTOR (Ser2481) (p = 0.017) and phosphoSRC (Thr24) (p = 0.020) protein expression. The recurrently deleted regions included 3p14.2 which was significantly associated with response to the PI3K/mTOR inhibitor BEZ235 (p=0.031). This region was found to be significantly correlated with MEK (p=0.042) and phosphoCDK2 (Thr160) (p=0.018) protein expression, and contained the putative tumor suppressor gene FHIT, a hydrolase involved with purine metabolism. Conclusions: TRIB1 is a potential oncogenic driver in CRC which may be associated with therapeutic resistance to platinum compounds. 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 885. doi:1538-7445.AM2012-885