FXYD3 functionally demarcates an ancestral breast cancer stem cell subpopulation with features of drug-tolerant persisters

The heterogeneity of cancer stem cells (CSCs) within tumors presents a challenge in therapeutic targeting. To decipher the cellular plasticity that fuels phenotypic heterogeneity, we undertook single-cell transcriptomics analysis in triple-negative breast cancer (TNBC) to identify subpopulations in CSCs. We found a subpopulation of CSCs with ancestral features that is marked by FXYD domain–containing ion transport regulator 3 (FXYD3), a component of the Na(+)/K(+) pump. Accordingly, FXYD3(+) CSCs evolve and proliferate, while displaying traits of alveolar progenitors that are normally induced during pregnancy. Clinically, FXYD3(+) CSCs were persistent during neoadjuvant chemotherapy, hence linking them to drug-tolerant persisters (DTPs) and identifying them as crucial therapeutic targets. Importantly, FXYD3(+) CSCs were sensitive to senolytic Na(+)/K(+) pump inhibitors, such as cardiac glycosides. Together, our data indicate that FXYD3(+) CSCs with ancestral features are drivers of plasticity and chemoresistance in TNBC. Targeting the Na(+)/K(+) pump could be an effective strategy to eliminate CSCs with ancestral and DTP features that could improve TNBC prognosis.