Discovering new drugs to target microsatellite instable (MSI) colorectal cancer (CRC) using the Connectivity Map (CMap)

Abstract

11087 Background: MSI tumors represent approximately 15% of CRC. Several preclinical and clinical studies have identified differences in response to 5-Fluorouracil and Irinotecan between Microsatellite Stable (MSS) and MSI tumors. CMap is a systems biology tool which enables researchers to match a gene expression signature defining a biologic state of interest with a database containing expression data obtained from different cell lines after being exposed to a panel of 164 small molecules. Our objective was to identify new compounds to target MSI tumors using CMap and to evaluate these candidates in the preclinical setting. Methods: We have used gene expression data generated from MSI tumors included in the Molecular Epidemiology of Colorectal Cancer study and from 2 signatures published previously (Watanabe et al and Koinuma et al). In addition, an aggregated signature was generated from the common genes found to be up and downregulated through the 3 signatures. The most active compounds selected for cytotoxicity assays fulfilled the following criteria: ≥2 negative scores in the global analysis using the CMap; ≥50% negative scores; and compounds highly ranked in terms of a summary measure obtained from aggregating p-values across the different signatures. CRC cell lines showing MSI due to mutations in mismatch repair (MMR) genes, MSI due to hypermethylation of the promoter of MLH1, and MSS were selected to perform cytotoxicity experiments. Cells were seeded in 96-well plates and exposed to 7 different concentrations of drug over 5 days. Results: 17-Allyamino-Geldamycin (17- AAG), which targets hsp90, and Trichostatin, which acts through HDAC inhibition, are novel small molecules predicted to preferentially target MSI CRC based on expression profiles and the CMap. Cell lines with hypermethylation of MLH1 were more sensitive to 17-AAG than MSS and MSI cell lines harboring mutations in MMR genes. No differences in IC50 concentrations were observed for Trichostatin between any groups. Conclusions: We report the application of CMap systems biology tool for discovering new small molecules to specifically target MSI CRC. Further investigation of 17-AAG in combination with standard chemotherapeutic agents is warranted for MSI colorectal cancers. No significant financial relationships to disclose.