Single-cell molecular subtyping reveals novel intratumor heterogeneity in human Basal-like breast cancer

Breast cancer is a molecularly heterogeneous disease composed of multiple intrinsic subtypes. Recent studies have highlighted the substantial intratumor heterogeneity of breast cancer, wherein malignant cells of distinct intrinsic subtypes co-exist within the same tumor. However, most existing subtyping methods are designed for bulk transcriptomic data and are therefore limited in their ability to resolve such intratumor heterogeneity at single-cell resolution. To address this gap, we develop UBS93, a computational framework that enables robust molecular subtyping of both bulk tumor samples and individual breast cancer cells. We rigorously validate UBS93 and demonstrate its superior performance relative to existing approaches, particularly in identifying the highly aggressive Claudin-low subtype. Applying UBS93 to single-cell RNA sequencing data from human Basal-like breast cancers, we identify the co-existence of Basal-like and Claudin-low cancer cell populations within the same tumor—a form of intratumor heterogeneity previously observed only in mouse models with genetically engineered RAS pathway alterations. Further analyses suggest that Claudin-low cancer cells originate from Basal-like population, with down-regulation of transcription factor ELF3 playing a pivotal role in the Basal-like/Claudin-low transition. Together, our findings establish UBS93 as a powerful tool for breast cancer subtyping and uncover a previously unrecognized layer of intratumor heterogeneity in human Basal-like breast cancer.