Embedding single-cell experimental conditions to reveal manifold structure of cancer drug perturbation effects

Previously, the effect of a drug on a cell population was measured based on simple metrics such as cell viability. However, as single-cell technologies are becoming more advanced, drug screen experiments can now be conducted with more complex readouts such as gene expression profiles of individual cells. The increasing complexity of measurements from these multi-sample experiments calls for more sophisticated analytical approaches than are currently available. We developed a novel method called PhEMD (Phenotypic Earth Mover's Distance) and show that it can be used to embed the space of drug perturbations on the basis of the drugs' effects on cell populations. When testing PhEMD on a newly-generated, 300-sample CyTOF kinase inhibition screen experiment, we find that the state space of the perturbation conditions is surprisingly low-dimensional and that the network of drugs demonstrates manifold structure. We show that because of the fairly simple manifold geometry of the 300 samples, we can accurately capture the full range of drug effects using a dictionary of only 30 experimental conditions. We also show that new drugs can be added to our PhEMD embedding using similarities inferred from other characterizations of drugs using a...Continue Reading