ICIsc: A Deep Learning Framework for Predicting Immune Checkpoint Inhibitor Response by Integrating scRNA-Seq and...

Immune checkpoint inhibitors (ICIs) targeting PD-1/PD-L1 and CTLA-4 are widely used in the treatment of several cancers and have significantly improved survival outcomes in responsive patients. However, a substantial proportion of patients fail to benefit from these therapies, underscoring the urgent need for accurate prediction of ICI response. We propose a deep learning framework, ICIsc, to accurately predict ICI response by integrating single-cell RNA sequencing (scRNA-seq) data with protein large language models. Specifically, patient representations are constructed using transcriptomic profiles and immune-related gene set scores as latent embedding features, while drug representations are derived from amino acid sequences of ICI encoded by the Evolutionary Scale Modeling 2 (ESM2). For bulk data, ICIsc employs a bilinear attention module to fuse patient and drug embeddings for response prediction. For scRNA-seq data, ICIsc infers cell-cell interactions using a single-sample network (SSN) approach and applies GATv2 to model immune microenvironment heterogeneity at the single-cell level. Benchmark evaluations and independent validation demonstrate that ICIsc consistently outperforms baseline models and exhibits robust generalization performance. SHAP-based interpretability analysis further identifies key genes (e.g., GAPDH) associated with immunotherapy response and patient prognosis. Overall, ICIsc provides an accurate and interpretable framework for predicting immunotherapy outcomes and elucidating underlying mechanisms.