Development and Validation of a Pan-Cancer Stromal Activity Score for Predicting Prognosis and Immunotherapy Response

Background: The tumor microenvironment (TME) plays a critical role in cancer progression and treatment response. Stromal components, including cancer-associated fibroblasts (CAFs), extracellular matrix (ECM), and angiogenesis, contribute to tumor aggressiveness. However, a comprehensive stromal activity score integrating multiple stromal dimensions for pan-cancer prognosis prediction is lacking. Methods: We developed a Stromal Activity Score (SAS) integrating five stromal dimensions: CAF signature (12 genes), ECM remodeling (15 genes), TGF-{beta} signaling (13 genes), angiogenesis (12 genes), and complement activation (11 genes). SAS was calculated using single-sample Gene Set Enrichment Analysis (ssGSEA) on TCGA pan-cancer data comprising 1,303 samples across 12 cancer types. Prognostic value was evaluated using Kaplan-Meier analysis and Cox regression. Immunotherapy response prediction was validated in two independent cohorts (IMvigor210, n=88; Liu2019, n=105). Results: Pan-cancer Cox regression demonstrated a significant association between SAS and overall survival (HR = 1.165, 95% CI: 1.065-1.275, P = 0.001). Per-cancer analysis identified BRCA (HR = 1.942, P = 0.022), STAD (HR = 1.684, P = 0.024), and LUSC (HR = 1.552, P = 0.038) as significant, though none survived FDR correction. SAS correlated strongly with ESTIMATE Stromal Score (Spearman {rho} = 0.835) and moderately with Immune Score ({rho} = 0.396). Immunotherapy validation showed consistent trends (IMvigor210: AUC = 0.602; Liu2019: AUC = 0.617). Time-dependent ROC analysis showed 1-year AUC = 0.596, 3-year = 0.579, 5-year = 0.559. Leave-one-out analysis identified angiogenesis removal as enhancing prognostic signal (HR = 3.737, P = 0.0002). Three distinct TME subtypes were identified with differential SAS profiles. Conclusions: SAS is a novel pan-cancer stromal activity score that captures TME biology with strong construct validity. Its clinical utility as a standalone biomarker remains modest, but it may complement existing immunotherapy biomarkers.