Transforming Histology into Virtual Multiplex Immunofluorescence to Decode Prognostic Spatial Immunity in Hepatocellular Carcinoma

Summary The spatial organization of the tumor immune microenvironment (TIME) drives hepatocellular carcinoma (HCC) prognosis but remains unquantifiable on routine H&E slides. Here, we present HCCExplorer, a deep learning framework that translates H&E into virtual multiplex immunofluorescence (mIF) and uses multi-modal graph learning to decode spatial survival signals. Trained on 30 H&E-mIF slide pairs, HCCExplorer evaluated a 1,813-slide multi-center cohort. It achieved superior overall survival stratification over clinical indices and state-of-the-art pathology and protein foundation models, yielding a concordance index of 0.71 and a Hazard Ratio (HR) of 15.46 ( P < 0.001), maintaining stability across three external cohorts. Beyond risk stratification, interpretation of model features identified M1 macrophage infiltration as a protective determinant (HR=0.40, P < 0.05). Furthermore, it uncovered a protective “Containment Niche” at the invasion frontier (HR=0.02, P < 0.01), featuring macrophages co-localizing with Foxp3+ Tregs and CD4+ T cells. Ultimately, HCCExplorer provides actionable, spatially-resolved biomarkers from conventional histology for precision HCC management.