Decoding breast cancer heterogeneity: a novel three-gene signature links intratumoral heterogeneity with tumor microenvironment and patient outcomes.

Breast cancer remains a leading cause of cancer-related mortality worldwide, with intratumoral heterogeneity (ITH) emerging as a critical determinant of treatment outcomes. While ITH's role in therapeutic resistance is increasingly recognized, its interactions with the tumor microenvironment and potential as a prognostic biomarker remain insufficiently explored. This study leverages comprehensive bioinformatic analyses of The Cancer Genome Atlas (TCGA) data to uncover novel ITH-associated prognostic markers in breast cancer. Using the DEPTH2 algorithm for ITH scoring, we demonstrated that high-ITH tumors correlate significantly with poor overall survival. Through differential expression analysis between high- and low-ITH groups, we discovered and validated a novel three-gene signature (CLIC6, SUSD3, and LTF) using Cox regression and stepAIC methodology. External validation using the METABRIC cohort confirmed the signature's robust prognostic significance. Notably, our signature revealed previously unrecognized associations between ITH and the tumor immune microenvironment (TIME), suggesting potential therapeutic implications. Further analysis uncovered significant associations between our ITH-based signature and specific cancer hallmarks, genetic alterations, and clinicopathological features. Our findings not only establish a practical prognostic tool but also provide novel insights into the intricate relationship between tumor heterogeneity and the microenvironment, highlighting potential therapeutic targets for personalized breast cancer treatment.