THR-6E: A Six-Gene Cell-of-Origin Signature Stratifies Risk and Predicts Systemic Therapy Response in ER+/HER2− Breast Cancer

ABSTRACT Background Genomic assays such as Oncotype DX, MammaPrint, and Prosigna have transformed risk stratification and treatment selection in early-stage, estrogen receptor-positive (ER+), HER2-negative breast cancers by enabling more precise prognostication and chemotherapy de-escalation in selected patients. However, their clinical utility is limited in lymph nodes positive disease. A major unmet need is the development of compact, mechanistically grounded biomarkers that extend risk and treatment-response prediction to clinically challenging ER+/HER2− subgroups, including lymph node–positive patients. Methods Building on a cell-of-origin framework, we previously established a 70-gene triple hormone receptor (THR; ER, AR, VDR) signature (THR-70) that reflects luminal epithelial differentiation programs and is prognostic across breast cancer subtypes. Here, we refined this framework using interactome-guided clustering to derive a six-gene cell-of-origin signature (THR-6E: KIF4A, KIF2C, CDC20, FAM64A, TPX2, and LMNB2). We evaluated the prognostic and predictive performance of THR-6E across >7,000 breast cancer cases from multiple independent cohorts, assessed treatment-response prediction using endocrine- and chemotherapy-annotated datasets, and performed independent validation in the I-SPY2 adaptive clinical trial. Findings THR-6E robustly stratifies relapse-free survival (RFS) in ER+/HER2− breast cancer independent of tumor grade, proliferation status, and subtype. Hazard ratios for RFS were 2.41 (p