Spherical Manifolds Capture Drug-Induced Changes in Tumor Cell Cycle Behavior

CDK4/6 inhibitors such as palbociclib block cell cycle progression and improve outcomes for many ER+/HER2- breast cancer patients. Unfortunately, many patients are initially resistant to the drug or develop resistance over time in part due to heterogeneity among individual tumor cells. To better understand these mechanisms of resistance, we used multiplex, single-cell imaging to profile cell cycle proteins in ER+ breast tumor cells under increasing palbociclib concentrations. We then applied spherical principal component analysis (SPCA), a dimensionality reduction method that leverages the inherently cyclical nature of the high-dimensional imaging data, to look for changes in cell cycle behavior in resistant cells. SPCA characterizes data as a hypersphere and provides a framework for visualizing and quantifying differences in cell cycles across treatment-induced perturbations. The hypersphere representations revealed shifts in the mean cell state and population heterogeneity. SPCA validated expected trends of CDK4/6 inhibitor response such as decreased expression of proliferation markers (Ki67, pRB), but also revealed potential mechanisms of resistance including increased expression of cyclin D1 and CDK2. Understanding the molecular mechanisms that allow treated tumor cells to evade arrest is critical for identifying targets of future therapies. Ultimately, we seek to further SPCA as a tool of precision medicine, targeting treatments by individual tumors, and extending this computational framework to interpret other cyclical biological processes represented by high-dimensional data.