Li, Y.; Diab, A. R.; Lamane, A.; Lindsay, J. R.; Rodig, S. J.; Irizarry, R. A.; Lotter, W.

Multiplex immunofluorescence (mIF) assays such as ImmunoProfile provide standardized quantification of prognostic immune markers but are costly and not routinely used in clinical settings. We developed a weakly-supervised AI model, HistoProfile, to estimate intratumoral cell densities of key immune biomarkers (CD8, FOXP3, PD-1, and PD-L1) and the PD-L1 tumor proportion score from routine H&E-stained whole-slide images. Trained on a large pan-cancer cohort with paired H&E and mIF data, HistoProfile discriminated biomarker-high from biomarker-low tumors in held-out samples and tumor-specific subgroups (AUROCs of 0.78-0.89 across biomarkers). Critically, the estimated biomarkers preserved prognostic stratification in downstream survival analyses, and showed cancer-specific survival associations across TCGA cohorts where mIF is unavailable. These findings support scalable H&E-based estimation of key immune biomarker measurements for large-scale immune profiling and risk stratification.