Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer

Triple-negative breast cancer, characterized by aggressive growth and high intratumor heterogeneity, presents a significant clinical challenge. Here, we use a lineage-tracing system, ClonMapper, which couples heritable clonal identifying tags with single-cell RNA-sequencing (scRNA-seq), to better elucidate the response to doxorubicin in a model of TNBC. We demonstrate that, while there is a dose-dependent reduction in overall clonal diversity, there is no pre-existing resistance signature among surviving clones. Separately, we found the existence of two transcriptomically distinct clonal subpopulations that remain through the course of treatment. Among clones persisting across multiple samples we identified divergent phenotypes, suggesting a response to treatment independent of clonal identity. Finally, a subset of clones harbor novel changes in expression following treatment. The clone and sample specific responses to treatment identified herein highlight the need for better personalized treatment strategies to overcome tumor heterogeneity. Targeted barcode sequencing of MDA-MB-231 cells with ClonMapper DNA barcode tags selected with doxorubicin treatment.