Clonal Lineage Tracing Reveals Distinct Invasive Subpopulations in Triple-Negative Breast Cancer

Metastatic dissemination in triple-negative breast cancer (TNBC) arises from extensive intratumoral heterogeneity, yet the clonal and transcriptional programs that underlie invasive behavior remain poorly defined. The field lacks experimental systems capable of simultaneously tracking the clonal identity and transcriptional state of invasive subpopulations. Here, we apply a clonal lineage-tracing platform coupled with single-cell RNA sequencing to resolve how subpopulations contribute to invasion in a model of TNBC. We demonstrate that invasion is driven by a subset of recurrent clones, indicating the presence of pre-existing subpopulations intrinsically primed for migratory behavior. Transcriptomic profiling further reveals two transcriptomically distinct invasive cell states that remain stable across independent selections. Targeted perturbations suppress these dominant invasive programs but enable invasion by alternative rare clones, demonstrating compensatory clonal dynamics in response to selective pressure. Together these findings show that invasive potential arises from stable clonal programs and that heterogenous tumors maintain invasive capacity through clonal replacement. Clonally resolved single-cell profiling provides a framework for dissecting invasive heterogeneity and highlights the need for therapeutic strategies that account for clone-specific behaviors and the dynamic restructuring of tumor subpopulations.