A Visually Interpretable Histopathology-Based Immune Model Predicts T-effector Biology and Response to Immune checkpoint inhibition in Clear Cell Renal Cell Carcinoma Clinical Trial and Contemporary Real-World Datasets
Immune checkpoint inhibitors (ICI) are central to the treatment of metastatic clear cell renal cell carcinoma (ccRCC), yet only a subset of patients derive durable benefit, and clinically deployable predictive biomarkers remain an unmet need. RNA-based T-effector signatures capture cytotoxic immune biology and have been associated with ICI response in clinical trial cohorts; however, their clinical implementation is limited by the marked spatial heterogeneity of ccRCC, as well as cost, long turnaround time, sample quality requirements, and limited accessibility. Here, we developed a visually interpretable deep learning (DL) model that predicts a T-cell-enriched immune score directly from hematoxylin and eosin (H&E)-stained whole-slide images. To overcome the inability of H&E morphology alone to distinguish lymphocyte subsets, we trained the model using multimodal spatial supervision from CD8, PAX8, and ERG IHC, which respectively identified cytotoxic T-cell-rich regions, tumor cells, and endothelial cells, thereby constraining immune predictions to relevant tumor microenvironmental niches. The resulting H&E DL Immune score was validated by pathologist review, comparison with held-out CD8 IHC annotations, and independent datasets. The H&E DL Immune score correlated with T-effector RNA scores across independent institutional and IMmotion150 clinical trial cohorts (spearman correlations of 0.726; p=5.90x10-15 and 0.706; p=4.04x10-19). As a proof of principle, the score was used to characterize associations with key biological features across large cohorts, including sarcomatoid differentiation, BAP1 and PBRM1 mutation status, and additional transcriptomic signatures. In IMmotion150 clinical trial cohort, a median-dichotomized H&E DL Immune score, similar to RNA-based T-effector score, was significantly associated with clinical benefit from atezulumab therapy. In contemporary institutional cohorts of patients treated with frontline ipilimumab plus nivolumab or in initial 3 lines of nivolumab monotherapy, patients in the top quartile of H&E DL Immune score had significantly longer progression-free survival. Collectively, these findings support a scalable and interpretable H&E-based biomarker that captures T-effector biology and can help identify patients with ccRCC more likely to benefit from ICIs.