Virtual spatial transcriptomics from histopathology enables prognostic and therapeutic response prediction in cancer
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Spatial transcriptomics reveals cellular heterogeneity, intercellular communication, and tissue organization, but its cost and limited accessibility restrict clinical use. Here, we present VISTA, a model that integrates multi-scale histological features and spatial context to infer spatial gene expression from H&E-stained tissue images. Across leave-one-section-out cross-validation and independent validation, VISTA robustly predicted thousands of genes and outperformed state-of-the-art methods. Beyond expression reconstruction, VISTA enabled clinically relevant downstream analyses. In TCGA breast cancer samples, it identified survival-associated genes, stratified prognostic risk groups, and revealed adverse tumor-associated spatial subtypes. In our in-house intrahepatic cholangiocarcinoma cohort, it preserved tumor–normal organization and identified CLDN4 and CYP3A4 as complementary spatial biomarkers. In HER2+ breast cancer, it predicted pathological response to neoadjuvant trastuzumab-based therapy and linked response-associated regions to immune and cytokine-related programs. These results support virtual spatial transcriptomics from routine histopathology for oncology applications.
