Cancer drug sensitivity prediction from routine histology images

Summary Drug sensitivity prediction models can aid in personalising cancer therapy, biomarker discovery, and drug design. Such models require survival data from randomized controlled trials which can be time consuming and expensive. In this proof-of-concept study, we demonstrate for the first time that deep learning can link histological patterns in whole slide images (WSIs) of Haematoxylin & Eosin (H&E) stained breast cancer sections with drug sensitivities inferred from cell lines. We employ patient-wise drug sensitivities imputed from gene expression based mapping of drug effects on cancer cell lines to train a deep learning model that predicts sensitivity to multiple drugs from WSIs. We show that it is possible to use routine WSIs to predict the drug sensitivity profile of a cancer patient for a number of approved and experimental drugs. We also show that the proposed approach can identify cellular and histological patterns associated with drug sensitivity profiles of cancer patients. Highlights Predicting drug sensitivity from routine histology images and cell lines Discovery of histology image patterns linked to drug sensitivity A novel deep learning pipeline for analysing drug sensitivity profiles