SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing

In this study, we devised a computational framework called Supervised Feature Learning and Scoring (SuperFeat) which enables the training of a machine learning model and evaluates the canonical cellular statuses/features in pathological tissues that underlie the progression of disease. This framework also enables the identification of potential drugs that target the presumed detrimental cellular features. This framework was constructed on the basis of an artificial neural network with the gene expression profiles serving as input nodes. The training data comprised single-cell RNA sequencing datasets that encompassed the specific cell lineage during the developmental progression of cell features. A few models of the canonical cancer-involved cellular statuses/features were tested by such framework. Finally, we illustrated the drug repurposing pipeline, utilizing the training parameters derived from the adverse cellular statuses/features, which yielded successful validation results both in vitro and in vivo. SuperFeat is accessible at https://github.com/weilin-genomics/rSuperFeat.