Ontogeny and Vulnerability of Lapatinib Drug-Tolerant Persisters in HER2-positive Breast Cancer

Despite advances in HER2-targeted therapeutics, resistance remains a significant clinical problem in HER2-positive (HER2+) breast cancer, especially in the metastatic setting. Drug-tolerant persisters (DTPs), a sub-population of cancer cells that survive via reversible, non-genetic mechanisms, are implicated in resistance to tyrosine kinase inhibitors (TKIs) in several cancer models, but DTPs for HER2-targeted TKIs have not been characterized extensively. We found that upon treatment with the TKI lapatinib, HER2+ breast cancer lines yielded DTPs with luminal-like or mesenchymal-like transcriptional programs and differential sensitivity to lapatinib/anti-estradiol combinations. Lentiviral barcoding and single cell RNA-sequencing indicate that HER2+/ER+ cells cycle stochastically through a pre-DTP state, characterized by a G0-like signature, which uniquely gives rise to DTPs upon lapatinib exposure. Overall design: BT474 and HCC1419 cells from untreated, 6h lapatinib treatment (6h) and 14-day lapatinib treatment (DTPs) were submitted for scRNA-seq. SKBR3, EFM192A, SUM225 parental cells were submitted for scRNA-seq. BT474, HCC1419, EFM192A and SKBR3 cells that were either untreated, treated 14 days with lapatinib or treated 14 days with tucatinib were submitted for RNA-seq.