A microRNA molecular modeling extension for prediction of colorectal cancer treatment

BACKGROUND: Several studies show that the regulatory impact of microRNAs (miRNAs) is an essential contribution to the pathogenesis of colorectal cancer (CRC). The expression levels of diverse miRNAs are associated with specific clinical diagnoses and prognoses of CRC. However, this association reveals very little actionable information with regard to how or whether to treat a CRC patient. To address this problem, we use miRNA expression data along with other molecular information to predict individual response of CRC cell lines and CRC patients. METHODS: A strategy has been developed to join four types of information: molecular, kinetic, genetic and treatment data for prediction of individual treatment response of CRC. RESULTS: Information on miRNA regulation, including miRNA target regulation and transcriptional regulation of miRNA, in integrated into an in silico molecular model for colon cancer. This molecular model is applied to study responses of seven CRC cell lines from NCI-60 to ten agents targeting signaling pathways. Predictive results of models without and with implemented miRNA information are compared and advantages are shown for the extended model. Finally, the extended model was applied to the data of 22 CRC patients to predict response to treatments of sirolimus and LY294002. The in silico results can also replicate the oncogenic and tumor suppression roles of miRNA on the therapeutic response as reported in the literature. CONCLUSIONS: In summary, the results reveal that detailed molecular events can be combined with individual genetic data, including gene/miRNA expression data, to enhance in silico prediction of therapeutic response of individual CRC tumors. The study demonstrates that miRNA information can be applied as actionable information regarding individual therapeutic response. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-015-1437-0) contains supplementary material, which is available to authorized users.