A disentangled transformer-based transfer learning framework to predict patient drug response from tumor single-cell transcriptomics.

Abstract

Intratumoral cellular heterogeneity limits therapeutic efficacy in cancer patients. Although single-cell transcriptomics offers high-resolution profiling, translating these insights into clinical drug response prediction remains challenging. Recently, transfer learning approaches have attempted to predict patient drug response by leveraging pre-clinical data. However, these approaches operate at the bulk level, often masking the cellular heterogeneity essential for prediction. In this study, we propose scTAPE, a disentangled transfer learning framework to predict patient drug response using tumor single-cell transcriptomics. scTAPE follows a pre-training and fine-tuning paradigm. During the pre-training stage, scTAPE uses a disentangled learning strategy to extract intrinsic pharmacological signals masked by confounding factors from the matched bulk and single-cell expression profiles. Subsequently, a supervised drug response model is trained on labeled cell-line data to fine-tune the aligned common embedding, thereby achieving cross-domain generalization to unseen datasets. Experimental results demonstrate that scTAPE successfully predicts drug response across cell-line datasets and two independent clinical cohorts, outperforming state-of-the-art single-cell-based predictors. Furthermore, by analyzing tumor cell subpopulations, scTAPE not only predicts patient drug response to both single and combination treatments but also identifies potential therapeutic agents targeting drug-resistant subpopulations. The implementation of scTAPE is available via https://github.com/xinliangSun/scTAPE.