Abstract Background: Despite therapeutic advances, patients with both estrogen receptor (ER) -positive and Human Epidermal growth factor Receptor 2 (HER2) -positive breast cancers have persistent clinical heterogeneity. We hypothesized that stromal-immune interactions within the tumor microenvironment (TME) drive differential treatment outcomes. Materials and methods: We analyzed 356 primary surgical HER2-positive tumors (treated with adjuvant trastuzumab) using gene expression panel profiling derived from formalin-fixed paraffin-embedded (FFPE) specimens. Unsupervised clustering of pathway enrichment levels was performed. The Combined Immune-Stromal Score (CISS) was developed, and we validated it for associations with recurrence-free survival (RFS) in both ER-positive and HER2-positive patients. Validation was performed using independent validation cohorts: PREDIX HER2 (neoadjuvant), SCAN-B, METABRIC, and TCGA. Results: Four biological subgroups were identified, characterized by differences in stromal markers (stromal), immune infiltration, cytokine and chemokine signaling, and antigen presentation (immune). Patients with Lowₛtromal and Lowᵢmmune tumors had significantly worse RFS compared to Lowₛtromal and Highᵢmmune (adjusted Hazard Ratio (HRadj) = 2. 55, 95% confidence interval (CI) = 1. 09-5. 95, p = 0. 03), and Highₛtromal and Lowᵢmmune (HRadj = 2. 30, 95% CI = 1. 18-4. 48, p = 0. 01). In both ER-positive and HER2-positive patients, each unit increase in CISS was associated with a 40% reduction in recurrence risk (HRadj = 0. 60, 95% CI = 0. 42-0. 86, p = 0. 00544), a finding consistently replicated across validation cohorts. Patients with low-CISS tumors (concurrent low stromal and low immune activity) demonstrated a worse prognosis (Log Rank p = 0. 0069). Conclusions: The Combined Immune-Stromal Score (CISS) is a novel gene expression-based signature that stratifies recurrence risk in early both ER-positive and HER2-positive breast cancer. Tumors with low CISS, characterized by concurrently low stromal and immune pathway activity, were associated with significantly poorer outcomes. These findings suggest that a suppressed TME may contribute to recurrence risk and highlight the potential of CISS as a prognostic tool and a basis for future studies exploring therapeutic vulnerabilities. Citation Format: q. yang, C. Rönnlund, C. Schagerholm Stanev, X. Chen, T. Foukakis, K. Wang, I. Fredriksson, R. Stephanie, E. G. Sifakis, J. Hartman. The Combined Immune-Stromal Score (CISS): A Novel Prognostic Gene Signature in Early both ER-positive and HER2-positive Breast Cancer abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32 (4 Suppl): Abstract nr PS3-11-24.
Yang et al. (Tue,) studied this question.