Learning the cellular activity representation based on gene regulatory networks for prediction of tumor response to drugs

Abstract

Predicting the response of tumor cells to anti-tumor drugs is critical to realizing cancer precision medicine. Currently, most existing methods ignore the regulatory relationships between genes and thus have unsatisfactory predictive performance. In this paper, we propose to predict anti-tumor drug efficacy via learning the activity representation of tumor cells based on a priori knowledge of gene regulation networks (GRNs). Specifically, the method simulates the cellular biosystem by synthesizing a cell-gene activity network and then infers a new low-dimensional activity representation for tumor cells from the raw high-dimensional expression profile. The simulated cell-gene network mainly comprises known gene regulatory networks collected from multiple resources and fuses tumor cells by linking them to hotspot genes that are over- or under-expressed in them. The resulting activity representation could not only reflect the shallow expression profile (hotspot genes) but also mines in-depth information of gene regulation activity in tumor cells before treatment. Finally, we build deep learning models on the activity representation for predicting drug efficacy in tumor cells. Experimental results on the benchmark GDSC dataset demonstrate the superior performance of the proposed method over SOTA methods with the highest AUC of 0.954 in the efficacy label prediction and the best R2 of 0.834 in the regression of half maximal inhibitory concentration (IC50) values, suggesting the potential value of the proposed method in practice.