Profiling Multiple CD8+ T-Cell Functional Dimensions Enhances Breast Cancer Immune Assessment

Abstract CD8+ T-cell abundance is insufficient to assess antitumor immunity and shows poor performance in predicting breast cancer prognosis and immunotherapy response, presumably owing to the complexity of CD8+ T-cell functionalities. While single-cell RNA sequencing (scRNA-seq) can dissect the multifaceted functions of CD8+ T cells for better immune assessment, its clinical application is limited. Herein, we developed bulk RNA-seq–based FuncDimen models from integrative analysis of scRNA-seq and matched bulk RNA-seq data, to evaluate CD8+ T-cell functionalities across 5 dimensions: tumor reactivity, cytotoxicity, IFN-γ secretion, proliferation, and apoptosis. The FuncDimen models quantifying different functional dimensions of CD8+ T cells were validated in our breast cancer cohort and external databases using immunofluorescence and imaging mass cytometry. We calculated the FuncAggre score by weighted aggregation of all 5 FuncDimen models to encapsulate the overall antitumor immunity. In our breast cancer cohort and external databases, FuncAggre score demonstrated superior predictive performance for breast cancer prognosis (time-dependent area under the curve [AUC]: 0.56-0.70) and immunotherapy response (AUC: 0.71-0.83) over other immune biomarkers, regardless of the breast cancer molecular subtype. Together, the FuncDimen models offer a refined assessment of antitumor immunity mediated by CD8+ T cells in the clinic, enhancing prognostic prediction and aiding personalized immunotherapy in breast cancer.