A biomarker based high throughput screen identifies small molecular weight modulators of the beta-catenin pathway

A217 We have developed a drug discovery system based on gene expression biomarkers to identify small molecule inhibitors of key signaling pathways, and used it to identify inhibitors of the beta-catenin pathway. Oncogenic activation of cell signaling pathways is a hallmark of cancer. While drugs have been successfully developed against a few of these pathways, these have been limited to those that contain conventionally druggable targets, in particular the kinases. Unfortunately, many of the key nodes in the important pathways are dominated by targets with no conventionally druggable domain such as transcription factors and adaptor proteins, or where the key nodes have yet to be clearly defined. We have developed a drug discovery system based on gene expression biomarkers to identify small molecule inhibitors of key signaling pathways, and used it to identify inhibitors of the beta-catenin pathway. The beta-catenin pathway plays a key role in the initiation and progression of cancer. Activating mutations have been found in many cancer types and it has been estimated that the beta-catenin pathway is abnormally activated in more than 85% of colon cancers, as well as in a large number of other cancer types. Mutations in the pathway lead to the constitutive activation of the beta-catenin protein, a transcriptional adaptor protein with no known enzymatic function. Small molecule inhibitors of the pathway were identified using a gene expression biomarker based high-throughput screening system. We treated a colon cancer cell line with siRNA against beta-catenin and identified a set of gene expression biomarkers that were correlated with the decrease in pathway activity. The gene based biomarkers were reduced down to a set of seven genes that were able to specifically identify small molecule compounds known to interrupt beta-catenin signaling. This biomarker signature was then used to screen a small molecule library of 80,000 compounds and positive compounds were selected for further study. A set of compounds were identified which induced a G1 cell cycle arrest, and inhibited the activity of the beta-catenin pathway either by decreasing active nuclear beta-catenin or causing the reduction of beta-catenin protein. Transcriptional profiling studies were used to characterize and categorize compounds by comparing full genome profiles to a database of hundreds of known reference small molecule compounds and to gene signatures descriptive of functional and pathway activity. This system has identified and characterized a set of compounds that are starting points for development of exciting new therapies for cancer that target the beta-catenin pathway. This method describes a new paradigm in drug discovery for targeting classically intractable pathways using biomarkers signatures directly correlated with the disease state.