A rare subset of primary tumor cells with concomitant hyper-activation of extracellular matrix remodeling and dsRNA-IFN1 signaling metastasizes in breast cancer.

Metastatic breast cancer (BC) has a poor prognosis and is largely considered incurable. A better understanding of the molecular determinants of BC metastasis could facilitate development of improved prevention and treatment strategies. We used lentiviral barcoding coupled to single-cell RNA sequencing to trace clonal and transcriptional evolution during BC metastasis and showed that metastases derive from rare pro-metastatic clones that are under-represented in primary tumors. Both low clonal fitness and high metastatic potential were independent of clonal origin. Differential expression and classification analyses revealed that the pro-metastatic phenotype was acquired by rare cells characterized by the concomitant hyper-activation of extracellular matrix remodeling and dsRNA-interferon signaling pathways. Notably, genetic silencing of key genes in these pathways (KCNQ1OT1 or IFI6, respectively) significantly impaired migration in vitro and metastasis in vivo, with marginal effects on cell proliferation and tumor growth. Gene expression signatures derived from the identified pro-metastatic genes predict metastatic progression in BC patients, independently of known prognostic factors. This study elucidates previously unknown mechanisms of BC metastasis and provides prognostic predictors and therapeutic targets for metastasis prevention.