Cross-Domain Feature Disentanglement for Interpretable Modeling of Tumor Microenvironment Impact on Drug Response

High-throughput screening technology has enabled the generation of large-scale drug responses across hundreds of cancer cell lines. There remains a significant gap between in vitro cell lines and actual tumors in vivo in terms of their response to drug treatments yet. This is because tumors consist of a complex cellular composition and histopathology structure, known as the tumor microenvironment (TME), which greatly impacts the drug cytotoxicity against tumor cells. To date, no study has focused on modeling the impact of the TME on clinical drug response. In this study, we postulated that the intricate complexity of an actual tumor can be conceptually simplified into two separable components: cancerous cells and the tumor microenvironment. This assumption allowed us to model the influence of these two constituent parts on drug response through feature disentanglement. We employed a domain adaptation network to decouple and extract features from tumor transcriptional profiles. Specifically, two denoising autoencoders were separately used to extract features from cell lines (source domain) and tumors (target domain) for partial domain alignment and feature decoupling. The private encoder was enforced to extract information only about the TME. Moreover, to ensure generalizability to novel drugs, we employed a graph attention network to learn the latent representation of drugs, enabling us to linearly model the drug perturbation on cellular state in latent space. We validated our model on a benchmark dataset and demonstrated its superior performance in predicting clinical drug response and dissecting the influence of the TME on drug efficacy.