Multidimensional profiling of drug-treated cells by Imaging Mass Cytometry

In pharmaceutical research, high-content screening is an integral part of lead candidate development. Drug response in vitro over 40 parameters including biomarkers, signaling molecules, cell morphological changes, proliferation indexes and toxicity in a single sample could significantly enhance discovery of new therapeutics. As a proof of concept, we present a workflow for multidimensional Imaging Mass Cytometry (IMC) and data processing with open source computational tools. CellProfiler was used to identify single cells through establishing cellular boundaries, followed by histoCAT (histology topography cytometry analysis toolbox) for extracting single-cell quantitative information visualized as t-SNE plots and heatmaps. Human breast cancer-derived cell lines SKBR3, HCC1143 and MCF-7 were screened for expression of cellular markers to generate digital images with a resolution comparable to conventional fluorescence microscopy. Predicted pharmacodynamic effects were measured in MCF-7 cells dosed with three target-specific compounds: growth stimulatory EGF, microtubule depolymerization agent nocodazole and genotoxic chemotherapeutic drug etoposide. We show strong pairwise correlation between nuclear markers pHistone3S28, Ki-67 and p4E-BP1T37/T46 in classified mitotic cells and anti-correlation with cell surface markers. Our study demonstrates that IMC data expands the number of measured parameters in single cells and brings higher-dimension analysis to the field of cell-based screening in early lead compound discovery.