Evaluating Drug Response in 3D Triple Negative Breast Cancer Tumoroids with High Content Imaging and Analysis

Abstract There is a critical need to develop methods for efficient testing of drug efficacy in patient-derived tumor samples to discover new therapeutics. Two-dimensional (2D) cell culture remains the primary method of drug screening, despite being considered less physiologically relevant than three-dimensional (3D) culture. Increased complexity and technical challenges of 3D systems have limited its widespread adoption as a primary screening method. In this study, we demonstrate methods for increased throughput, imaging and automation in 3D assays that are suitable for compound screening using patient-derived samples. In addition, we show analysis approaches and descriptors that allow gain more information about disease phenotypes and compound effects. We measured responses to drug treatment in 3D tumoroids for cytotoxicity and altered morphology. Tumoroids were formed from primary cells isolated from a patient-derived tumor explant, TU-BcX-4IC, that represents metaplastic breast cancer with a triple-negative subtype and treated with 165 compounds, of approved cancer drugs, at multiple concentrations. We characterize multiple quantitative descriptors for tumor phenotypes and compound effects. Cell Painting method was used for 3D tumoroids for evaluation of phenotypic effects. Eight compounds were detected that demonstrated effects at low concentrations (10nM), including romidepsin, trametinib, bortezomib, carfilzomib, panobinostat, which will be further investigated as potential drug candidates.